Summary
Biology
Debian Med bioinformatics packages
This metapackage will install Debian packages for use in molecular biology,
structural biology and other biological sciences.
Description
For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:
If you discover a project which looks like a good candidate for Debian Med
to you, or if you have prepared an unofficial Debian package, please do not hesitate to
send a description of that project to the Debian Med mailing list
Links to other tasks
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Debian Med Biology packages
Official Debian packages with high relevance
abacas
close gaps in genomic alignments from short reads
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Versions of package abacas |
Release | Version | Architectures |
stretch | 1.3.1-3 | all |
buster | 1.3.1-5 | all |
sid | 1.3.1-9 | all |
jessie | 1.3.1-2 | all |
trixie | 1.3.1-9 | all |
bookworm | 1.3.1-9 | all |
bullseye | 1.3.1-9 | all |
Debtags of package abacas: |
role | program |
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License: DFSG free
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ABACAS (Algorithm Based Automatic Contiguation of Assembled Sequences)
intends to rapidly contiguate (align, order, orientate), visualize and
design primers to close gaps on shotgun assembled contigs based on a
reference sequence.
ABACAS uses MUMmer to find alignment positions and identify syntenies
of assembled contigs against the reference. The output is then processed
to generate a pseudomolecule taking overlapping contigs and gaps in to
account. ABACAS generates a comparison file that can be used to
visualize ordered and oriented contigs in ACT. Synteny is represented by
red bars where colour intensity decreases with lower values of percent
identity between comparable blocks. Information on contigs such as the
orientation, percent identity, coverage and overlap with other contigs
can also be visualized by loading the outputted feature file on ACT.
Topics: Probes and primers
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abpoa
adaptive banded Partial Order Alignment
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Versions of package abpoa |
Release | Version | Architectures |
trixie | 1.5.3-1 | amd64,arm64,ppc64el |
sid | 1.5.3-1 | amd64,arm64,ppc64el |
bookworm | 1.4.1-3 | amd64,arm64,ppc64el |
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License: DFSG free
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abPOA is an extended version of Partial Order Alignment (POA) that performs
adaptive banded dynamic programming (DP) with an SIMD implementation. abPOA
can perform multiple sequence alignment (MSA) on a set of input sequences and
generate a consensus sequence by applying the heaviest bundling algorithm to
the final alignment graph.
abPOA can generate high-quality consensus sequences from error-prone long
reads and offer significant speed improvement over existing tools.
abPOA supports three alignment modes (global, local, extension) and flexible
scoring schemes that allow linear, affine and convex gap penalties. It right
now supports SSE2/SSE4.1/AVX2 vectorization.
For more information please refer to the paper1 published in Bioinformatics.
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abyss
de novo, parallel, sequence assembler for short reads
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Versions of package abyss |
Release | Version | Architectures |
bullseye | 2.2.5+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.3.10-1 | amd64,arm64,mips64el,ppc64el,riscv64 |
sid | 2.3.10-1 | amd64,arm64,mips64el,ppc64el,riscv64 |
jessie | 1.5.2-1 (non-free) | amd64 |
bookworm | 2.3.5+dfsg-2 | amd64,arm64,mips64el,ppc64el,s390x |
stretch | 2.0.2-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.1.5-7 | amd64,arm64,armhf,i386 |
stretch-backports | 2.1.5-7~bpo9+1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package abyss: |
role | program |
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License: DFSG free
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ABySS is a de novo, parallel, sequence assembler that is designed for
short reads. It may be used to assemble genome or transcriptome
sequence data. Parallelization is achieved using MPI, OpenMP and
pthread.
Please cite:
Shaun D. Jackman, Benjamin P. Vandervalk, Hamid Mohamadi, Justin Chu, Sarah Yeo, S. Austin Hammond, Golnaz Jahesh, Hamza Khan, Lauren Coombe, Rene L. Warren and İnanç Birol:
"ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter".
(PubMed,eprint)
Genome Research
27(5):768-777
(2017)
Topics: Sequence assembly
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acedb-other
retrieval of DNA or protein sequences
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Versions of package acedb-other |
Release | Version | Architectures |
bullseye | 4.9.39+dfsg.02-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 4.9.39+dfsg.02-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 4.9.39+dfsg.02-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 4.9.39+dfsg.01-5 | amd64,armel,armhf,i386 |
stretch | 4.9.39+dfsg.02-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 4.9.39+dfsg.02-4 | amd64,arm64,armhf,i386 |
Debtags of package acedb-other: |
biology | nuceleic-acids |
field | biology, biology:bioinformatics |
role | program |
scope | utility |
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License: DFSG free
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This package collects all those smallish applications that acedb collects
under its 'other' target of its Makefile.
efetch: presumably short for 'entry fetch' collects sequence information
from common DNA and protein databases.
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adapterremoval
rapid adapter trimming, identification, and read merging of gene sequences
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Versions of package adapterremoval |
Release | Version | Architectures |
sid | 2.3.3-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.3.3-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 2.2.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.2.3-1 | amd64,arm64,armhf,i386 |
trixie | 2.3.3-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 2.3.1-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 2.3.4 |
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License: DFSG free
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This program searches for and removes remnant adapter sequences from High-
Throughput Sequencing (HTS) data and (optionally) trims low quality
bases from the 3' end of reads following adapter removal. AdapterRemoval
can analyze both single end and paired end data, and can be used to
merge overlapping paired-ended reads into (longer) consensus sequences.
Additionally, the AdapterRemoval may be used to recover a consensus
adapter sequence for paired-ended data, for which this information is
not available.
The package is enhanced by the following packages:
multiqc
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adun-core
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Versions of package adun-core |
Release | Version | Architectures |
stretch | 0.81-9 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.81-13 | amd64,arm64,armhf,i386 |
sid | 0.81-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.81-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.81-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.81-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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Adun is a biomolecular simulator that also includes data management and
analysis capabilities. It was developed at the Computational Biophysics
and Biochemistry Laboratory, a part of the Research Unit on Biomedical
Informatics of the UPF.
This package contains the AdunCore program and the Adun server. If
you want the graphical UI frontend, install the adun.app package.
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aegean
integrated genome analysis toolkit
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Versions of package aegean |
Release | Version | Architectures |
stretch | 0.15.2+dfsg-1 | amd64,arm64,armel,armhf,i386,mipsel,ppc64el,s390x |
buster | 0.16.0+dfsg-1 | amd64,arm64,armhf,i386 |
bullseye | 0.16.0+dfsg-2 | amd64,arm64,armel,armhf,i386,mipsel,ppc64el,s390x |
bookworm | 0.16.0+dfsg-2 | amd64,arm64,armel,armhf,i386,mipsel,ppc64el,s390x |
trixie | 0.16.0+dfsg-4 | amd64,arm64,armel,armhf,i386,ppc64el,s390x |
sid | 0.16.0+dfsg-4 | amd64,arm64,armel,armhf,i386,ppc64el,s390x |
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License: DFSG free
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The AEGeAn Toolkit is designed for the Analysis and Evaluation of Genome
Annotations. The toolkit includes a variety of analysis programs, e.g. for
comparing distinct sets of gene structure annotations (ParsEval), computation
of gene loci (LocusPocus) and more.
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aevol
digital genetics model to run Evolution Experiments in silico
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Versions of package aevol |
Release | Version | Architectures |
buster | 5.0-2 | amd64,arm64,armhf,i386 |
sid | 5.0+ds-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 5.0+ds-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 4.4-1 | amd64,armel,armhf,i386 |
stretch | 4.4-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 5.0+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 5.0+ds-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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Aevol is a digital genetics model: populations of digital organisms are
subjected to a process of selection and variation, which creates a
Darwinian dynamics.
By modifying the characteristics of selection (e.g. population size,
type of environment, environmental variations) or variation (e.g.
mutation rates, chromosomal rearrangement rates, types of
rearrangements, horizontal transfer), one can study experimentally the
impact of these parameters on the structure of the evolved organisms.
In particular, since Aevol integrates a precise and realistic model of
the genome, it allows for the study of structural variations of the
genome (e.g. number of genes, synteny, proportion of coding sequences).
The simulation platform comes along with a set of tools for analysing
phylogenies and measuring many characteristics of the organisms and
populations along evolution.
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alien-hunter
Interpolated Variable Order Motifs to identify horizontally acquired DNA
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Versions of package alien-hunter |
Release | Version | Architectures |
bullseye | 1.7-8 | all |
jessie | 1.7-3 | all |
stretch | 1.7-5 | all |
buster | 1.7-7 | all |
bookworm | 1.7-10 | all |
trixie | 1.7-10 | all |
sid | 1.7-10 | all |
Debtags of package alien-hunter: |
field | biology, biology:structural |
role | program |
scope | utility |
use | analysing |
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License: DFSG free
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Alien_hunter is an application for the prediction of putative
Horizontal Gene Transfer (HGT) events with the implementation of
Interpolated Variable Order Motifs (IVOMs). An IVOM approach
exploits compositional biases using variable order motif distributions
and captures more reliably the local composition of a sequence compared
to fixed-order methods. Optionally the predictions can be parsed into a
2-state 2nd order Hidden Markov Model (HMM), in a change-point detection
framework, to optimize the localization of the boundaries of the
predicted regions. The predictions (embl format) can be automatically
loaded into Artemis genome viewer freely available at:
http://www.sanger.ac.uk/Software/Artemis/.
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alter-sequence-alignment
genomic sequences ALignment Transformation EnviRonment
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Versions of package alter-sequence-alignment |
Release | Version | Architectures |
buster | 1.3.4-2 | all |
stretch | 1.3.3+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.3.4-6 | all |
bullseye | 1.3.4-4 | all |
sid | 1.3.4-8 | all |
trixie | 1.3.4-8 | all |
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License: DFSG free
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ALTER (ALignment Transformation EnviRonment) is a tool to transform
between multiple sequence alignment formats. ALTER focuses on the
specifications of mainstream alignment and analysis programs rather than
on the conversion among more or less specific formats.
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altree
program to perform phylogeny-based association and localization analysis
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Versions of package altree |
Release | Version | Architectures |
buster | 1.3.1-7 | amd64,arm64,armhf,i386 |
stretch | 1.3.1-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.3.1-2 | amd64,armel,armhf,i386 |
sid | 1.3.2-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.3.2-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.3.2-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.3.1-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package altree: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program, shared-lib |
scope | utility |
use | analysing, comparing |
works-with-format | plaintext |
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License: DFSG free
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ALTree was designed to perform association detection and localization of
susceptibility sites using haplotype phylogenetic trees: first, it allows the
detection of an association between a candidate gene and a disease, and second,
it enables to make hypothesis about the susceptibility loci.
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amap-align
Protein multiple alignment by sequence annealing
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Versions of package amap-align |
Release | Version | Architectures |
jessie | 2.2-4 | amd64,armel,armhf,i386 |
stretch | 2.2-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.2+git20080214.600fc29+dfsg-1 | amd64,arm64,armhf,i386 |
bullseye | 2.2+git20080214.600fc29+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.2+git20080214.600fc29+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.2+git20080214.600fc29+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.2+git20080214.600fc29+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package amap-align: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing, comparing |
works-with-format | plaintext |
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License: DFSG free
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AMAP is a command line tool to perform multiple alignment of peptidic
sequences. It utilizes posterior decoding, and a sequence-annealing
alignment, instead of the traditional progressive alignment method. It is
the only alignment program that allows one to control the sensitivity /
specificity tradeoff. It is based on the ProbCons source code, but
uses alignment metric accuracy and eliminates the consistency
transformation.
The Java visualisation tool of AMAP 2.2 is not yet packaged in Debian.
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ampliconnoise
removal of noise from 454 sequenced PCR amplicons
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Versions of package ampliconnoise |
Release | Version | Architectures |
bookworm | 1.29-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.29-2 | amd64,armel,armhf,i386 |
stretch | 1.29-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.29-8 | amd64,arm64,armhf,i386 |
sid | 1.29-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.29-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.29-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package ampliconnoise: |
role | program |
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License: DFSG free
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AmpliconNoise is a package of applications to clean up high-throughput
sequence data. It consists of three main parts:
Pyronoise - does flowgram-based clustering to spot misreads
SeqNoise - removes PCR point mutations
Perseus - removes PCR chimeras without the need for a set of reference
sequences
Previously there was a standalone "Pyronoise" by the same authors and
this package includes an updated version. There is also a "Denoiser"
in Qiime which is related but distinct.
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andi
Efficient Estimation of Evolutionary Distances
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Versions of package andi |
Release | Version | Architectures |
trixie | 0.14-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.14-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.14-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.13-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 0.10-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.12-4 | amd64,arm64,armhf,i386 |
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License: DFSG free
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This is the andi program for estimating the evolutionary distance
between closely related genomes. These distances can be used to rapidly
infer phylogenies for big sets of genomes. Because andi does not compute
full alignments, it is so efficient that it scales even up to thousands
of bacterial genomes.
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anfo
Short Read Aligner/Mapper from MPG
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Versions of package anfo |
Release | Version | Architectures |
jessie | 0.98-4 | amd64,armel,armhf,i386 |
sid | 0.98-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x |
stretch | 0.98-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.98-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.98-7 | amd64,arm64,armhf,i386 |
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License: DFSG free
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Anfo is a mapper in the spirit of Soap/Maq/Bowtie, but its implementation takes
more after BLAST/BLAT. It's most useful for the alignment of sequencing reads
where the DNA sequence is somehow modified (think ancient DNA or bisulphite
treatment) and/or there is more divergence between sample and reference than
what fast mappers will handle gracefully (say the reference genome is missing
and a related species is used instead).
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any2fasta
convert various sequence formats to FASTA
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Versions of package any2fasta |
Release | Version | Architectures |
sid | 0.4.2-2 | all |
bookworm | 0.4.2-2 | all |
trixie | 0.4.2-2 | all |
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License: DFSG free
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Established tools like readseq and seqret from EMBOSS, both create mangled
IDs containing | or . characters, and there is no way to fix this behaviour.
This resultes in inconsitences between .gbk and .fna versions of files in
pipelines.
This script uses only core Perl modules, has no other dependencies like
Bioperl or Biopython, and runs very quickly.
It supports the following input formats:
1. Genbank flat file, typically .gb, .gbk, .gbff (starts with LOCUS)
2. EMBL flat file, typically .embl, (starts with ID)
3. GFF with sequence, typically .gff, .gff3 (starts with ##gff)
4. FASTA DNA, typically .fasta, .fa, .fna, .ffn (starts with >)
5. FASTQ DNA, typically .fastq, .fq (starts with @)
6. CLUSTAL alignments, typically .clw, .clu (starts with CLUSTAL or MUSCLE)
7. STOCKHOLM alignments, typically .sth (starts with # STOCKHOLM)
8. GFA assembly graph, typically .gfa (starts with ^[A-Z]\t)
Files may be compressed with:
1. gzip, typically .gz
2. bzip2, typically .bz2
3. zip, typically .zip
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aragorn
tRNA and tmRNA detection in nucleotide sequences
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Versions of package aragorn |
Release | Version | Architectures |
trixie | 1.2.41-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.2.38-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.2.38-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.2.38-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.2.36-4 | amd64,armel,armhf,i386 |
sid | 1.2.41-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.2.38-2 | amd64,arm64,armhf,i386 |
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License: DFSG free
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The program employs heuristic algorithms to predict tRNA secondary structure,
based on homology with recognized tRNA consensus sequences and ability to form
a base-paired cloverleaf. tmRNA genes are identified using a modified version
of the BRUCE program.
Topics: Functional, regulatory and non-coding RNA
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arden
specificity control for read alignments using an artificial reference
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Versions of package arden |
Release | Version | Architectures |
bookworm | 1.0-5 | all |
jessie | 1.0-1 | amd64,armel,armhf,i386 |
stretch | 1.0-3 | all |
buster | 1.0-4 | all |
bullseye | 1.0-5 | all |
trixie | 1.0-6 | all |
sid | 1.0-6 | all |
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License: DFSG free
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ARDEN (Artificial Reference Driven Estimation of false positives in NGS
data) is a novel benchmark that estimates error rates based on real
experimental reads and an additionally generated artificial reference
genome. It allows the computation of error rates specifically for a
dataset and the construction of a ROC-curve. Thereby, it can be used to
optimize parameters for read mappers, to select read mappers for a
specific problem or also to filter alignments based on quality
estimation.
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ariba
Antibiotic Resistance Identification By Assembly
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Versions of package ariba |
Release | Version | Architectures |
trixie | 2.14.7+ds-5 | amd64,arm64,mips64el,ppc64el,riscv64 |
stretch-backports | 2.13.3+ds-1~bpo9+1 | amd64 |
buster | 2.13.3+ds-1 | amd64 |
stretch | 2.6.1+ds-1 | amd64 |
bullseye | 2.14.6+ds-1 | amd64,arm64,mips64el,ppc64el |
sid | 2.14.7+ds-5 | amd64,arm64,mips64el,ppc64el,riscv64 |
bookworm | 2.14.6+ds-5 | amd64,arm64,mips64el,ppc64el |
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License: DFSG free
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ARIBA is a tool that identifies antibiotic resistance genes by running local
assemblies.
The input is a FASTA file of reference genes and paired sequencing reads. ARIBA
reports which of the reference genes were found, plus detailed information on
the quality of the assemblies and any variants between the sequencing reads
and the reference genes.
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art-nextgen-simulation-tools
simulation tools to generate synthetic next-generation sequencing reads
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Versions of package art-nextgen-simulation-tools |
Release | Version | Architectures |
trixie | 20160605+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 20160605+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 20160605+dfsg-3 | amd64,arm64,armhf,i386 |
sid | 20160605+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 20160605+dfsg-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 20160605+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
ART is a set of simulation tools to generate synthetic next-generation
sequencing reads. ART simulates sequencing reads by mimicking real
sequencing process with empirical error models or quality profiles
summarized from large recalibrated sequencing data. ART can also
simulate reads using user own read error model or quality profiles. ART
supports simulation of single-end, paired-end/mate-pair reads of three
major commercial next-generation sequencing platforms: Illumina's
Solexa, Roche's 454 and Applied Biosystems' SOLiD. ART can be used to
test or benchmark a variety of method or tools for next-generation
sequencing data analysis, including read alignment, de novo assembly,
SNP and structure variation discovery. ART was used as a primary tool
for the simulation study of the 1000 Genomes Project . ART is
implemented in C++ with optimized algorithms and is highly efficient in
read simulation. ART outputs reads in the FASTQ format, and alignments
in the ALN format. ART can also generate alignments in the SAM
alignment or UCSC BED file format. ART can be used together with genome
variants simulators (e.g. VarSim) for evaluating variant calling tools
or methods.
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artemis
genome browser and annotation tool
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Versions of package artemis |
Release | Version | Architectures |
trixie | 18.2.0+dfsg-4 | all |
sid | 18.2.0+dfsg-4 | all |
stretch | 16.0.17+dfsg-1 | all |
bookworm | 18.2.0+dfsg-3 | all |
bullseye | 18.1.0+dfsg-3 | amd64 |
buster | 17.0.1+dfsg-2 | amd64 |
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License: DFSG free
|
Artemis is a genome browser and annotation tool that allows visualisation of
sequence features, next generation data and the results of analyses within the
context of the sequence, and also its six-frame translation.
This package includes the Artemis genome browser, the Artemis Comparison
Tool (ACT), and the DNAplotter and BamView utilities.
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artfastqgenerator
outputs artificial FASTQ files derived from a reference genome
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Versions of package artfastqgenerator |
Release | Version | Architectures |
stretch | 0.0.20150519-2 | all |
buster | 0.0.20150519-3 | all |
sid | 0.0.20150519-5 | all |
bullseye | 0.0.20150519-4 | all |
trixie | 0.0.20150519-5 | all |
bookworm | 0.0.20150519-4 | all |
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License: DFSG free
|
ArtificialFastqGenerator takes the reference genome (in FASTA format) as
input and outputs artificial FASTQ files in the Sanger format. It can
accept Phred base quality scores from existing FASTQ files, and use them
to simulate sequencing errors. Since the artificial FASTQs are derived
from the reference genome, the reference genome provides a gold-standard
for calling variants (Single Nucleotide Polymorphisms (SNPs) and
insertions and deletions (indels)). This enables evaluation of a Next
Generation Sequencing (NGS) analysis pipeline which aligns reads to the
reference genome and then calls the variants.
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assembly-stats
get assembly statistics from FASTA and FASTQ files
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Versions of package assembly-stats |
Release | Version | Architectures |
sid | 1.0.1+ds-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.0.1+ds-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.0.1+ds-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.0.1+ds-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
|
Get statistics from a list of files.
Detection of FASTA or FASTQ format of each file is automatic from the
file contents, so file names and extensions are irrelevant.
The default output format is human readable. You can change the output
format and ignore sequences shorter than a given length.
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assemblytics
detect and analyze structural variants from a genome assembly
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Versions of package assemblytics |
Release | Version | Architectures |
bookworm | 1.2.1+dfsg-1 | all |
trixie | 1.2.1+dfsg-2 | all |
buster | 1.0+ds-1 | all |
bullseye | 1.0+ds-2 | all |
sid | 1.2.1+dfsg-2 | all |
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License: DFSG free
|
Assemblytics incorporates a unique anchor filtering approach to increase
robustness to repetitive elements, and identifies six classes of variants
based on their distinct alignment signatures. Assemblytics can be applied
both to comparing aberrant genomes, such as human cancers, to a reference,
or to identify differences between related species.
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atac
genome assembly-to-assembly comparison
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Versions of package atac |
Release | Version | Architectures |
bullseye | 0~20150903+r2013-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0~20150903+r2013-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0~20150903+r2013-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 0~20150903+r2013-6 | amd64,arm64,armhf,i386 |
trixie | 0~20150903+r2013-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 0~20150903+r2013-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
atac computes a one-to-one pairwise alignment of large DNA sequences. It first
finds the unique k-mers in each sequence, chains them to larger blocks, and
fills in spaces between blocks. It was written primarily to transfer
annotations between different assemblies of the human genome.
The output is a set of ungapped 'matches', and a set of gapped 'runs' formed
from the matches. Each match or run associates one sequence with the other
sequence. The association is 'unique', in that there is no other (sizeable)
associations for either sequence. Thus, large repeats and duplications are not
present in the output - they appear as unmapped regions.
Though the output is always pairwise, atac can cache intermediate results to
speed a comparisons of multiple sequences.
This package is part of the Kmer suite.
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ataqv
ATAC-seq QC and visualization
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Versions of package ataqv |
Release | Version | Architectures |
trixie | 1.3.1+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
bullseye | 1.2.1+ds-1 | amd64,arm64,armhf,i386,mips64el,mipsel,ppc64el |
bookworm | 1.3.0+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
sid | 1.3.1+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
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License: DFSG free
|
A toolkit for measuring and comparing ATAC-seq results, made in the
Parker lab at the University of Michigan. They wrote it to help
understand how well their ATAC-seq assays had worked, and to make it
easier to spot differences that might be caused by library prep or
sequencing.
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atropos
NGS read trimming tool that is specific, sensitive, and speedy
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Versions of package atropos |
Release | Version | Architectures |
bookworm | 1.1.31+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
sid | 1.1.32+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
trixie | 1.1.32+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
bullseye | 1.1.29+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
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License: DFSG free
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Atropos is tool for specific, sensitive, and speedy trimming of NGS
reads. It is a fork of the venerable Cutadapt read trimmer, with the
primary improvements being:
1. Multi-threading support, including an extremely fast "parallel
write" mode.
2. Implementation of a new insert alignment-based trimming algorithm
for paired-end reads that is substantially more sensitive and
specific than the original Cutadapt adapter alignment-based
algorithm. This algorithm can also correct mismatches between the
overlapping portions of the reads.
3. Options for trimming specific types of data (miRNA, bisulfite-seq).
4. A new command ('detect') that will detect adapter sequences and
other potential contaminants.
5. A new command ('error') that will estimate the sequencing error
rate, which helps to select the appropriate adapter- and quality-
trimming parameter values.
6. A new command ('qc') that generates read statistics similar to
FastQC. The trim command can also compute read statistics both
before and after trimming (using the '--stats' option).
7. Improved summary reports, including support for serialization
formats (JSON, YAML, pickle), support for user-defined templates
(via the optional Jinja2 dependency), and integration with MultiQC.
8. The ability to merge overlapping reads (this is experimental and
the functionality is limited).
9. The ability to write the summary report and log messages to
separate files.
10. The ability to read SAM/BAM files and read/write interleaved
FASTQ files.
11. Direct trimming of reads from an SRA accession.
12. A progress bar, and other minor usability enhancements.
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augur
pipeline components for real-time virus analysis
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Versions of package augur |
Release | Version | Architectures |
bullseye | 11.0.0-1 | all |
trixie | 24.4.0-1 | all |
bookworm | 20.0.0-1 | all |
sid | 24.4.0-1 | all |
buster-backports | 6.4.2-2~bpo10+1 | all |
upstream | 27.0.0 |
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License: DFSG free
|
The nextstrain project is an attempt to make flexible informatic
pipelines and visualization tools to track ongoing pathogen evolution as
sequence data emerges. The nextstrain project derives from nextflu,
which was specific to influenza evolution.
nextstrain is comprised of three components:
- fauna: database and IO scripts for sequence and serological data
- augur: informatic pipelines to conduct inferences from raw data
- auspice: web app to visualize resulting inferences
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augustus
gene prediction in eukaryotic genomes
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Versions of package augustus |
Release | Version | Architectures |
bookworm | 3.5.0+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 3.5.0+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 3.5.0+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 3.2.3+dfsg-1 | amd64,arm64,armel,i386,mips64el,mipsel,ppc64el |
buster | 3.3.2+dfsg-2 | amd64,arm64,armhf |
bullseye | 3.4.0+dfsg2-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
AUGUSTUS is a software for gene prediction in eukaryotic genomic sequences
that is based on a generalized hidden Markov model (HMM), a probabilistic
model of a sequence and its gene structure. After learning gene structures
from a reference annotation, AUGUSTUS uses the HMM to recognize genes in a new
sequence and annotates it with the regions of identified genes. External hints,
e.g. from RNA sequencing, EST or protein alignments etc. can be used to guide
and improve the gene finding process. The result is the set of most likely gene
structures that comply with all given user constraints, if such gene
structures exist.
AUGUSTUS already includes prebuilt HMMs for many species, as well as scripts
to train custom models using annotated genomes.
Topics: Gene transcripts; Gene and protein families
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autodock
analysis of ligand binding to protein structure
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Versions of package autodock |
Release | Version | Architectures |
bullseye | 4.2.6-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 4.2.6-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 4.2.6-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 4.2.6-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 4.2.6-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 4.2.6-2 | amd64,armel,armhf,i386 |
buster | 4.2.6-6 | amd64,arm64,armhf,i386 |
Debtags of package autodock: |
field | biology, biology:structural |
interface | commandline |
role | program |
scope | utility |
use | analysing |
works-with | 3dmodel |
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License: DFSG free
|
AutoDock is a prime representative of the programs addressing the
simulation of the docking of fairly small chemical ligands to rather big
protein receptors. Earlier versions had all flexibility in the ligands
while the protein was kept rather ridgid. This latest version 4 also
allows for a flexibility of selected sidechains of surface residues,
i.e., takes the rotamers into account.
The AutoDock program performs the docking of the ligand to a set of
grids describing the target protein. AutoGrid pre-calculates these grids.
The package is enhanced by the following packages:
autogrid
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autodock-vina
docking of small molecules to proteins
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Versions of package autodock-vina |
Release | Version | Architectures |
buster | 1.1.2-5 | amd64,arm64,armhf,i386 |
stretch | 1.1.2-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.2.3-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.1.2-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.1.2-3 | amd64,armel,armhf,i386 |
trixie | 1.2.5-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.2.5-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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AutoDock Vina is a program to support drug discovery, molecular
docking and virtual screening of compound libraries. It offers
multi-core capability, high performance and enhanced accuracy
and ease of use.
The same institute also developed autodock, which is widely used.
O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy
of docking with a new scoring function, efficient optimization and
multithreading, Journal of Computational Chemistry 31 (2010) 455-461
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autogrid
pre-calculate binding of ligands to their receptor
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Versions of package autogrid |
Release | Version | Architectures |
bookworm | 4.2.6-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 4.2.6-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 4.2.6-2 | amd64,armel,armhf,i386 |
buster | 4.2.6-6 | amd64,arm64,armhf,i386 |
sid | 4.2.6-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 4.2.6-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 4.2.6-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package autogrid: |
field | biology, biology:structural |
interface | commandline |
role | program |
scope | utility |
use | analysing |
works-with | 3dmodel |
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License: DFSG free
|
The AutoDockSuite addresses the molecular analysis of the docking of
a smaller chemical compounds to their receptors of known three-dimensional
structure.
The AutoGrid program performs pre-calculations for the docking of a
ligand to a set of grids that describe the effect that the protein has
on point charges. The effect of these forces on the ligand is then
analysed by the AutoDock program.
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avogadro
Molecular Graphics and Modelling System
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Versions of package avogadro |
Release | Version | Architectures |
jessie | 1.0.3-10.1 | amd64,armel,armhf,i386 |
stretch | 1.2.0-1+deb9u1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.2.0-4 | amd64,arm64,armhf,i386 |
bullseye | 1.93.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.97.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.99.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.99.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package avogadro: |
field | chemistry |
role | program |
uitoolkit | qt |
use | viewing |
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License: DFSG free
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Avogadro is a molecular graphics and modelling system targeted at molecules
and biomolecules. It can visualize properties like molecular orbitals or
electrostatic potentials and features an intuitive molecular builder.
Features include:
- Molecular modeller with automatic force-field based geometry optimization
- Molecular Mechanics including constraints and conformer searches
- Visualization of molecular orbitals and general isosurfaces
- Visualization of vibrations and plotting of vibrational spectra
- Support for crystallographic unit cells
- Input generation for the Gaussian, GAMESS and MOLPRO quantum chemistry
packages
- Flexible plugin architecture and Python scripting
File formats Avogadro can read include PDB, XYZ, CML, CIF, Molden, as well as
Gaussian, GAMESS and MOLPRO output.
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axe-demultiplexer
Trie-based DNA sequencing read demultiplexer
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Versions of package axe-demultiplexer |
Release | Version | Architectures |
sid | 0.3.3+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.3.3+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.3.3+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 0.3.3+dfsg-1 | amd64,arm64,armhf,i386 |
bullseye | 0.3.3+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 0.3.2+dfsg1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
Axe very rapidly selects the optimal barcode present in a sequence read, even
in the presence of sequencing errors. The algorithm is able to handle
combinatorial barcoding, barcodes of differing length, and several mismatches
per barcode.
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baitfisher
software package for designing hybrid enrichment probes
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Versions of package baitfisher |
Release | Version | Architectures |
buster | 1.2.7+git20180107.e92dbf2+dfsg-1 | amd64,arm64,armhf,i386 |
bullseye | 1.2.7+git20190123.241d060+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.2.7+git20211020.de26d5c+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.2.7+git20211020.de26d5c+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.2.7+git20211020.de26d5c+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
The BaitFisher package consists of two programs: BaitFisher and BaitFilter.
BaitFisher was been designed to construct hybrid enrichment baits from
multiple sequence alignments (MSAs) or annotated features in MSAs. The main
goal of BaitFisher is to avoid redundancy in the construction of baits by
designing fewer baits in conserved regions of the MSAs and designing more baits
in variable regions. This makes use of the fact that hybrid enrichment baits
can differ to some extends from the target region, which they should capture
in the enrichment procedure.
By specifying the allowed distance between baits and the sequences in the MSAs
the user can control the allowed bait-to-target distance and the degree of
reduction in the number of baits that are designed.
See the BaitFisher paper for details.
BaitFilter was designed (i) to determine whether baits bind unspecifically to
a reference genome, (ii) to filter baits that only have partial length matches
to a reference genome, (iii) to determine the optimal bait region in a MSA and
to convert baits to a format that can be uploaded at a bait constructing
company. The optimal bait region can be the most conserved region in the MSA
or the region with the highest number of sequences without gaps or ambiguous
nucleotides.
Please cite:
Christoph Mayer, Manuela Sann, Alexander Donath, Martin Meixner, Lars Podsiadlowski, Ralph S. Peters, Malte Petersen, Karen Meusemann, Karsten Liere, Johann-Wolfgang Wägele, Bernhard Misof, Christoph Bleidorn, Michael Ohl and Oliver Niehuis:
BaitFisher: A Software Package for Multispecies Target DNA Enrichment Probe Design.
(PubMed,eprint)
Mol. Biol. Evol.
33(7):1875-1886
(2016)
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bali-phy
Bayesian Inference of Alignment and Phylogeny
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Versions of package bali-phy |
Release | Version | Architectures |
trixie | 3.6.1+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
experimental | 4.0~beta16+dfsg-1 | amd64,arm64,i386,mips64el,ppc64el,riscv64,s390x |
experimental | 4.0~beta2+dfsg-1 | armhf |
buster | 3.4+dfsg-1 | amd64,arm64,armhf,i386 |
sid | 3.6.1+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 3.6.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.6.1+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
BAli-Phy estimates multiple sequence alignments and evolutionary trees
from unaligned DNA, amino acid, or codon sequences. BAli-Phy uses MCMC
to estimate evolutionary trees, positive selection, and branch lengths
while averaging over alternative alignments. BAli-Phy can display
alignment ambiguity graphically in an alignment uncertainty (AU) plot.
BAli-Phy can also estimate phylogenies from a fixed alignment (like MrBayes
and BEAST) using substitution models like GTR+gamma. BAli-Phy automatically
estimates relative rates for each gene.
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ballview
free molecular modeling and molecular graphics tool
|
Versions of package ballview |
Release | Version | Architectures |
bookworm | 1.5.0+git20180813.37fc53c-11 | amd64,arm64,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.4.3~beta1-3 | amd64,arm64,armel,armhf,i386,mips,ppc64el,s390x |
jessie | 1.4.2+20140406-1 | amd64,armel,armhf,i386 |
buster | 1.5.0+git20180813.37fc53c-3 | amd64,arm64,i386 |
bullseye | 1.5.0+git20180813.37fc53c-6 | amd64,arm64,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.5.0+git20180813.37fc53c-11 | amd64,arm64,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 1.5.0+git20220524.d85d2dd |
Debtags of package ballview: |
interface | x11 |
role | program |
uitoolkit | qt |
x11 | application |
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License: DFSG free
|
BALLView provides fast OpenGL-based visualization of molecular structures,
molecular mechanics methods (minimization, MD simulation using the
AMBER, CHARMM, and MMFF94 force fields), calculation and visualization
of electrostatic properties (FDPB) and molecular editing features.
BALLView can be considered a graphical user interface on the basis of
BALL (Biochemical Algorithms Library) with a focus on the most common
demands of protein chemists and biophysicists in particular. It is
developed in the groups of Hans-Peter Lenhof (Saarland University,
Saarbruecken, Germany) and Oliver Kohlbacher (University of Tuebingen,
Germany). BALL is an application framework in C++ that has been
specifically designed for rapid software development in Molecular
Modeling and Computational Molecular Biology. It provides an extensive
set of data structures as well as classes for Molecular Mechanics,
advanced solvation methods, comparison and analysis of protein
structures, file import/export, and visualization.
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bamclipper
Remove gene-specific primer sequences from SAM/BAM alignments
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Versions of package bamclipper |
Release | Version | Architectures |
bookworm | 1.0.0-3 | all |
trixie | 1.0.0-3 | all |
sid | 1.0.0-3 | all |
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License: DFSG free
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Remove gene-specific primer sequences from SAM/BAM alignments of PCR
amplicons by soft-clipping.
bamclipper.sh soft-clips gene-specific primers from BAM alignment file based
on genomic coordinates of primer pairs in BEDPE format.
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bamkit
tools for common BAM file manipulations
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Versions of package bamkit |
Release | Version | Architectures |
bullseye | 0.0.1+git20170413.ccd079d-2 | all |
bookworm | 0.0.1+git20170413.ccd079d-3 | all |
trixie | 0.0.1+git20170413.ccd079d-3 | all |
sid | 0.0.1+git20170413.ccd079d-3 | all |
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License: DFSG free
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This package provides some Python3 tools for common BAM file
manipulations.
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bamtools
toolkit for manipulating BAM (genome alignment) files
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Versions of package bamtools |
Release | Version | Architectures |
buster | 2.5.1+dfsg-3 | amd64,arm64,armhf,i386 |
trixie | 2.5.2+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 2.3.0+dfsg-2 | amd64,armel,armhf,i386 |
sid | 2.5.2+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.5.2+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 2.4.1+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.5.1+dfsg-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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BamTools facilitates research analysis and data management using BAM
files. It copes with the enormous amount of data produced by current
sequencing technologies that is typically stored in compressed, binary
formats that are not easily handled by the text-based parsers commonly
used in bioinformatics research.
BamTools provides both a C++ API for BAM file support as well as a
command-line toolkit.
This is the bamtools command-line toolkit.
Available bamtools commands:
convert Converts between BAM and a number of other formats
count Prints number of alignments in BAM file(s)
coverage Prints coverage statistics from the input BAM file
filter Filters BAM file(s) by user-specified criteria
header Prints BAM header information
index Generates index for BAM file
merge Merge multiple BAM files into single file
random Select random alignments from existing BAM file(s), intended more
as a testing tool.
resolve Resolves paired-end reads (marking the IsProperPair flag as needed)
revert Removes duplicate marks and restores original base qualities
sort Sorts the BAM file according to some criteria
split Splits a BAM file on user-specified property, creating a new BAM
output file for each value found
stats Prints some basic statistics from input BAM file(s)
The package is enhanced by the following packages:
multiqc
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bandage
Bioinformatics Application for Navigating De novo Assembly Graphs Easily
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Versions of package bandage |
Release | Version | Architectures |
bookworm | 0.9.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.8.1-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.8.1-1 | amd64,arm64,armhf,i386 |
sid | 0.9.0-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.9.0-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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Bandage is a GUI program that allows users to interact with the assembly
graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and
others.
De novo assembly graphs contain not only assembled contigs but
also the connections between those contigs, which were previously not
easily accessible. Bandage visualises assembly graphs, with connections,
using graph layout algorithms. Nodes in the drawn graph, which represent
contigs, can be automatically labelled with their ID, length or depth.
Users can interact with the graph by moving, labelling and colouring
nodes. Sequence information can also be extracted directly from the
graph viewer. By displaying connections between contigs, Bandage opens
up new possibilities for analysing and improving de novo assemblies that
are not possible by looking at contigs alone.
More information and download links are on the Bandage website:
rrwick.github.io/Bandage
The package is relevant to the field of genome assembly.
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barrnap
rapid ribosomal RNA prediction
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Versions of package barrnap |
Release | Version | Architectures |
bookworm | 0.9+dfsg-3 | all |
trixie | 0.9+dfsg-4 | all |
buster | 0.9+dfsg-1 | all |
stretch | 0.7+dfsg-2 | all |
sid | 0.9+dfsg-4 | all |
bullseye | 0.9+dfsg-2 | all |
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License: DFSG free
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Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of
ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea
(5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).
It takes FASTA DNA sequence as input, and writes GFF3 as output. It uses the
NHMMER tool that comes with HMMER 3.1 for HMM searching in RNA:DNA style.
Multithreading is supported and one can expect roughly linear speed-ups
with more CPUs.
Topics: Functional, regulatory and non-coding RNA
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bbmap
BBTools genomic aligner and other tools for short sequences
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Versions of package bbmap |
Release | Version | Architectures |
trixie | 39.13+dfsg-1 | all |
buster-backports | 38.63+dfsg-1~bpo10+1 | all |
bullseye | 38.90+dfsg-1 | all |
bookworm | 39.01+dfsg-2 | all |
sid | 39.13+dfsg-1 | all |
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License: DFSG free
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The BBTools are a collection of small programs to solve recurrent
tasks for the creative handling of short biological RNA/DNA sequences.
This suite may be best known for its mapper, which is also the name of
the project on sourceforge, but several tools have been added over time.
All tools are multi-threaded, implemented platform-independently in Java:
BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling
arbitrarily large genomes with millions of scaffolds. Handles Illumina,
PacBio, 454, and other reads; very high sensitivity and tolerant of
errors and numerous large indels.
BBNorm: Kmer-based error-correction and normalization tool.
Dedupe: Simplifies assemblies by removing duplicate or contained
subsequences that share a target percent identity.
Reformat: Reformats reads between fasta/fastq/scarf/fasta+qual/sam,
interleaved/paired, and ASCII-33/64, at over 500 MB/s.
BBDuk: Filters, trims, or masks reads with kmer matches to an
artifact/contaminant file.
The package is enhanced by the following packages:
multiqc
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bcalm
de Bruijn compaction in low memory
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Versions of package bcalm |
Release | Version | Architectures |
trixie | 2.2.3-5 | amd64,arm64,mips64el,ppc64el,riscv64 |
bookworm | 2.2.3-4 | amd64,arm64,mips64el,ppc64el |
bullseye | 2.2.3-1 | amd64,arm64,i386,mips64el,ppc64el,s390x |
sid | 2.2.3-5 | amd64,arm64,mips64el,ppc64el,riscv64 |
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License: DFSG free
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A bioinformatics tool for constructing the compacted de Bruijn graph
from sequencing data.
This is the parallel version of the BCALM software using gatb-core
library.
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bcftools
genomic variant calling and manipulation of VCF/BCF files
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Versions of package bcftools |
Release | Version | Architectures |
sid | 1.20-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch-backports | 1.8-1~bpo9+1 | amd64,arm64,armel,armhf,mips64el,mipsel,ppc64el |
stretch | 1.3.1-1 | amd64,arm64,armel,mips64el,mipsel,ppc64el |
bullseye | 1.11-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
buster | 1.9-1 | amd64,arm64,armhf |
trixie | 1.20-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.16-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
upstream | 1.21 |
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License: DFSG free
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BCFtools is a set of utilities that manipulate variant calls in the
Variant Call Format (VCF) and its binary counterpart BCF. All commands work
transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
The package is enhanced by the following packages:
multiqc
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beads
2-DE electrophoresis gel image spot detection
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Versions of package beads |
Release | Version | Architectures |
sid | 1.1.22-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.1.22-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.1.18+dfsg-3 | amd64,arm64,armhf,i386 |
bullseye | 1.1.20-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.1.22-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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Beads is a program for spot detection on 2-D gel images. It is based on
an analogy with beads flowing uphill on the surface of the gel image and
on the analysis of their paths (Langella & Zivy, 2008).
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beagle
Genotype calling, genotype phasing and imputation of ungenotyped markers
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Versions of package beagle |
Release | Version | Architectures |
stretch | 4.1~160727-86a+dfsg-1 | all |
trixie | 241029-1 | all |
bookworm | 220722-1 | all |
sid | 241029-1 | all |
bullseye | 5.1-200518+dfsg-1 | all |
buster | 5.0-180928+dfsg-1+deb10u1 | all |
upstream | 241217 |
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License: DFSG free
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Beagle performs genotype calling, genotype phasing, imputation of ungenotyped
markers, and identity-by-descent segment detection. Genotypic imputation works
on phased haplotypes using a Li and Stephens haplotype frequency model.
Beagle also implements the Refined IBD algorithm for detecting
homozygosity-by-descent (HBD) and identity-by-descent (IBD) segments.
The package is enhanced by the following packages:
beagle-doc
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beast-mcmc
Bayesian MCMC phylogenetic inference
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Versions of package beast-mcmc |
Release | Version | Architectures |
sid | 1.10.4+dfsg-6 | all |
bookworm | 1.10.4+dfsg-5 | all |
jessie | 1.8.0-1 (contrib) | all |
stretch | 1.8.4+dfsg.1-1 | all |
bullseye | 1.10.4+dfsg-2 | all |
buster | 1.10.4+dfsg-1 | all |
trixie | 1.10.4+dfsg-5 | all |
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License: DFSG free
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BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
sequences. It is entirely orientated towards rooted, time-measured
phylogenies inferred using strict or relaxed molecular clock models. It
can be used as a method of reconstructing phylogenies but is also a
framework for testing evolutionary hypotheses without conditioning on a
single tree topology. BEAST uses MCMC to average over tree space, so that
each tree is weighted proportional to its posterior probability. Included
is a simple to use user-interface program for setting up standard
analyses and a suit of programs for analysing the results.
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beast2-mcmc
Bayesian MCMC phylogenetic inference
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Versions of package beast2-mcmc |
Release | Version | Architectures |
bookworm | 2.7.3+dfsg-1 | all |
stretch | 2.4.4+dfsg-1 | all |
buster | 2.5.1+dfsg-2 | all |
sid | 2.7.6+dfsg-1 | all |
trixie | 2.7.6+dfsg-1 | all |
bullseye | 2.6.3+dfsg-2 | all |
upstream | 2.7.7 |
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License: DFSG free
|
BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
sequences. It is entirely orientated towards rooted, time-measured
phylogenies inferred using strict or relaxed molecular clock models. It
can be used as a method of reconstructing phylogenies but is also a
framework for testing evolutionary hypotheses without conditioning on a
single tree topology. BEAST uses MCMC to average over tree space, so that
each tree is weighted proportional to its posterior probability. Included
is a simple to use user-interface program for setting up standard
analyses and a suit of programs for analysing the results.
This is no new upstream version of beast-mcmc (1.x) but rather a rewritten
version.
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bedops
high-performance genomic feature operations
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Versions of package bedops |
Release | Version | Architectures |
trixie | 2.4.41+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch-backports | 2.4.35+dfsg-1~bpo9+1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2.4.41+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.4.41+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.4.39+dfsg1-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.4.35+dfsg-1 | amd64,arm64,armhf,i386 |
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License: DFSG free
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BEDOPS is a suite of tools to address common questions raised in genomic
studies, mostly with regard to overlap and proximity relationships between
data sets.
It aims to be scalable and flexible, facilitating the efficient and accurate
analysis and management of large-scale genomic data.
Please cite:
Shane Neph, M. Scott Kuehn, Alex P. Reynolds, Eric Haugen, Robert E. Thurman, Audra K. Johnson, Eric Rynes, Matthew T. Maurano, Jeff Vierstra, Sean Thomas, Richard Sandstrom, Richard Humbert and John A. Stamatoyannopoulos:
BEDOPS: high-performance genomic feature operations.
(PubMed,eprint)
28(14):1919-1920
(2012)
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bedtools
suite of utilities for comparing genomic features
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Versions of package bedtools |
Release | Version | Architectures |
buster | 2.27.1+dfsg-4 | amd64,arm64,armhf |
bookworm | 2.30.0+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.31.1+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.31.1+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 2.26.0+dfsg-3 | amd64,arm64,armel,i386,mips64el,mipsel,ppc64el |
jessie | 2.21.0-1 | amd64,armhf,i386 |
bullseye | 2.30.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package bedtools: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | suite |
use | analysing, comparing, converting, filtering |
works-with | biological-sequence |
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License: DFSG free
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The BEDTools utilities allow one to address common genomics tasks such as
finding feature overlaps and computing coverage. The utilities are largely
based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using
BEDTools, one can develop sophisticated pipelines that answer complicated
research questions by streaming several BEDTools together.
The groupBy utility is distributed in the filo package.
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belvu
multiple sequence alignment viewer and phylogenetic tool
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Versions of package belvu |
Release | Version | Architectures |
bullseye | 4.44.1+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 4.44.1+dfsg-7.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 4.44.1+dfsg-3 | amd64,arm64,armhf,i386 |
sid | 4.44.1+dfsg-7.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 4.44.1+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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Belvu is a multiple sequence alignment viewer and phylogenetic tool with
an extensive set of user-configurable modes to color residues.
- View multiple sequence alignments.
- Residues can be coloured by conservation, with user-configurable
cutoffs and colours.
- Residues can be coloured by residue type (user-configurable).
- Colour schemes can be imported or exported.
- Swissprot (or PIR) entries can be fetched by double clicking.
- The position in the alignment can be easily tracked.
- Manual deletion of rows and columns.
- Automatic editing of rows and columns based on customisable criteria:
- removal of all-gap columns;
- removal of all gaps;
- removal of redundant sequences;
- removal of a column by a user-specified percentage of gaps;
- filtering of sequences by percent identity;
- removal of sequences by a user-specified percentage of gaps;
- removal of partial sequences (those starting or ending with
gaps); and
- removal of columns by conservation (with user-specified
upper/lower cutoffs).
- The alignment can be saved in Stockholm, Selex, MSF or FASTA format.
- Distance matrices between sequences can be generated using a variety
of distance metrics.
- Distance matrices can be imported or exported.
- Phylogenetic trees can be constructed based on various distance-based
tree reconstruction algorithms.
- Trees can be saved in New Hampshire format.
- Belvu can perform bootstrap phylogenetic reconstruction.
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berkeley-express
Streaming quantification for high-throughput sequencing
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Versions of package berkeley-express |
Release | Version | Architectures |
bookworm | 1.5.3+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.5.3+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.5.2+dfsg-1 | amd64,arm64,armhf,i386 |
sid | 1.5.3+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.5.3+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.5.1-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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eXpress is a streaming tool for quantifying the abundances of a set of
target sequences from sampled subsequences. Example applications include
transcript-level RNA-Seq quantification, allele-specific/haplotype
expression analysis (from RNA-Seq), transcription factor binding
quantification in ChIP-Seq, and analysis of metagenomic data. It is
based on an online-EM algorithm that results in space (memory)
requirements proportional to the total size of the target sequences and
time requirements that are proportional to the number of sampled
fragments. Thus, in applications such as RNA-Seq, eXpress can accurately
quantify much larger samples than other currently available tools
greatly reducing computing infrastructure requirements. eXpress can be
used to build lightweight high-throughput sequencing processing
pipelines when coupled with a streaming aligner (such as Bowtie), as
output can be piped directly into eXpress, effectively eliminating the
need to store read alignments in memory or on disk.
In an analysis of the performance of eXpress for RNA-Seq data, it was
observed that this efficiency does not come at a cost of accuracy.
eXpress is more accurate than other available tools, even when limited
to smaller datasets that do not require such efficiency. Moreover, like
the Cufflinks program, eXpress can be used to estimate transcript
abundances in multi-isoform genes. eXpress is also able to resolve
multi-mappings of reads across gene families, and does not require a
reference genome so that it can be used in conjunction with de novo
assemblers such as Trinity, Oases, or Trans-ABySS. The underlying model
is based on previously described probabilistic models developed for
RNA-Seq but is applicable to other settings where target sequences are
sampled, and includes parameters for fragment length distributions,
errors in reads, and sequence-specific fragment bias.
eXpress can be used to resolve ambiguous mappings in other
high-throughput sequencing based applications. The only required inputs
to eXpress are a set of target sequences and a set of sequenced
fragments multiply-aligned to them. While these target sequences will
often be gene isoforms, they need not be. Haplotypes can be used as the
reference for allele-specific expression analysis, binding regions for
ChIP-Seq, or target genomes in metagenomics experiments. eXpress is
useful in any analysis where reads multi-map to sequences that differ in
abundance.
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bifrost
parallel construction, indexing and querying of de Bruijn graphs
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Versions of package bifrost |
Release | Version | Architectures |
sid | 1.3.1-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
trixie | 1.3.1-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
upstream | 1.3.5 |
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License: DFSG free
|
Bifrost is a command-line tool for sequencing that features a broad
range of functions, such as indexing, editing, and querying the graph,
and includes a graph coloring method that maps each k-mer of the graph
to the genomes it occurs in.
- Build, index, color and query the compacted de Bruijn graph
- No need to build the uncompacted de Bruijn graph
- Reads or assembled genomes as input
- Output graph in GFA (can be visualized with Bandage), FASTA or binary
- Graph cleaning: short tip clipping, etc.
- Multi-threaded
- No parameters to estimate with other tools
- Exact or approximate k-mer search of queries
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bio-eagle
Haplotype phasing within a genotyped cohort or using a phased reference panel
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Versions of package bio-eagle |
Release | Version | Architectures |
buster | 2.4.1-1 | amd64 |
sid | 2.4.1-3 | amd64,i386 |
stretch | 2.3-3 | amd64,i386 |
trixie | 2.4.1-3 | amd64,i386 |
bullseye | 2.4.1-3 | amd64,i386 |
bookworm | 2.4.1-3 | amd64,i386 |
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License: DFSG free
|
Eagle estimates haplotype phase either within a genotyped cohort or using a
phased reference panel. The basic idea of the Eagle1 algorithm is to harness
identity-by-descent among distant relatives—which is pervasive at very large
sample sizes but rare among smaller numbers of samples—to rapidly call phase
using a fast scoring approach. In contrast, the Eagle2 algorithm analyzes a
full probabilistic model similar to the diploid Li-Stephens model used by
previous HMM-based methods.
Please note: The executable was renamed to bio-eagle because of a name clash.
Please read more about this in /usr/share/doc/bio-eagle/README.Debian.
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bio-rainbow
clustering and assembling short reads for bioinformatics
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Versions of package bio-rainbow |
Release | Version | Architectures |
bookworm | 2.0.4+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.0.4+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.0.4+dfsg-1 | amd64,arm64,armhf,i386 |
stretch | 2.0.4-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2.0.4+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 2.0.4+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
|
Efficient tool for clustering and assembling short reads,
especially for RAD.
Rainbow is developed to provide an ultra-fast and memory-efficient
solution to clustering and assembling short reads produced by RAD-seq.
First, Rainbow clusters reads using a spaced seed method. Then, Rainbow
implements a heterozygote calling like strategy to divide potential
groups into haplotypes in a top-down manner. long a guided tree, it
iteratively merges sibling leaves in a bottom-up manner if they are
similar enough. Here, the similarity is defined by comparing the 2nd
reads of a RAD segment. This approach tries to collapse heterozygote
while discriminate repetitive sequences. At last, Rainbow uses a greedy
algorithm to locally assemble merged reads into contigs. Rainbow not
only outputs the optimal but also suboptimal assembly results. Based on
simulation and a real guppy RAD-seq data, it is shown that Rainbow is
more competent than the other tools in dealing with RAD-seq data.
|
|
bio-tradis
analyse the output from TraDIS analyses of genomic sequences
|
Versions of package bio-tradis |
Release | Version | Architectures |
sid | 1.4.5+dfsg2-2 | all |
trixie | 1.4.5+dfsg2-2 | all |
buster | 1.4.1+dfsg-1 | all |
bullseye | 1.4.5+dfsg2-1 | all |
bookworm | 1.4.5+dfsg2-1 | all |
stretch-backports | 1.3.3+dfsg-3~bpo9+1 | all |
|
License: DFSG free
|
Bio-Tradis contains a set of tools to analyse the output from
TraDIS analyses.
The Bio-Tradis analysis pipeline is implemented as an extensible Perl
library which can either be used as is, or as a basis for the
development of more advanced analysis tools.
Please note: You need to manually install BioConductor Edger which can
not be distributed by Debian in recent version since it is using
non-distributable code locfit.
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|
bio-vcf
domain specific language (DSL) for processing the VCF format
|
Versions of package bio-vcf |
Release | Version | Architectures |
bookworm | 0.9.5-3 | all |
trixie | 0.9.5-3 | all |
sid | 0.9.5-3 | all |
bullseye | 0.9.5-2 | all |
|
License: DFSG free
|
Bio-vcf provides a domain specific language (DSL) for processing the
VCF format. Record named fields can be queried with regular
expressions, e.g.
sample.dp>20 and rec.filter !~ /LowQD/ and rec.tumor.bcount[rec.alt]>4
Bio-vcf is a new generation VCF parser, filter and converter. Bio-vcf
is not only very fast for genome-wide (WGS) data, it also comes with a
really nice filtering, evaluation and rewrite language and it can
output any type of textual data, including VCF header and contents in
RDF and JSON.
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bioawk
extension of awk for biological sequence analysis
|
Versions of package bioawk |
Release | Version | Architectures |
sid | 1.0-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.0-4+deb12u1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.0-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
Bioawk is an extension to Brian Kernighan's awk, adding the support of
several common biological data formats, including optionally gzip'ed BED, GFF,
SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a
few built-in functions and an command line option to use TAB as the
input/output delimiter. When the new functionality is not used, bioawk is
intended to behave exactly the same as the original BWK awk.
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biobambam2
tools for early stage alignment file processing
|
Versions of package biobambam2 |
Release | Version | Architectures |
sid | 2.0.185+ds-2 | amd64,i386,mips64el,ppc64el,riscv64 |
bookworm | 2.0.185+ds-1 | amd64,arm64,i386,ppc64el |
bullseye | 2.0.179+ds-1 | amd64,arm64,i386,ppc64el |
trixie | 2.0.185+ds-2 | amd64,i386,mips64el,ppc64el,riscv64 |
upstream | 2.0.185-release-20221211202123 |
|
License: DFSG free
|
This package contains some tools for processing BAM files, including
bamsormadup: parallel sorting and duplicate marking
bamcollate2: reads BAM and writes BAM reordered such that alignment
or collated by query name
bammarkduplicates: reads BAM and writes BAM with duplicate alignments
marked using the BAM flags field
bammaskflags: reads BAM and writes BAM while masking (removing) bits
from the flags column
bamrecompress: reads BAM and writes BAM with a defined compression
setting. This tool is capable of multi-threading.
bamsort: reads BAM and writes BAM resorted by coordinates or
query name
bamtofastq: reads BAM and writes FastQ; output can be collated
or uncollated by query name
The package is enhanced by the following packages:
multiqc
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|
biosyntax
Syntax Highlighting for Computational Biology (metapackage)
|
Versions of package biosyntax |
Release | Version | Architectures |
bookworm | 1.0.0b-4 | all |
trixie | 1.0.0b-6 | all |
sid | 1.0.0b-6 | all |
buster | 1.0.0b-1 | all |
bullseye | 1.0.0b-2 | all |
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License: DFSG free
|
Syntax highlighting for computational biology to bring you intuitively close
to your data. BioSyntax supports .sam, .flagstat, .vcf, .fasta, .fastq, .faidx
, .clustal, .pdb, .gtf, .bed files & more.
This is a metapackage depending on all bioSyntax plugins.
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bitseq
Bayesian Inference of Transcripts from Sequencing Data
|
Versions of package bitseq |
Release | Version | Architectures |
sid | 0.7.5+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.7.5+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.7.5+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.7.5+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.7.5+dfsg-4 | amd64,arm64,armhf,i386 |
|
License: DFSG free
|
BitSeq is an application for inferring expression levels of individual
transcripts from sequencing (RNA-Seq) data and estimating differential
expression (DE) between conditions. An advantage of this approach is the
ability to account for both technical uncertainty and intrinsic biological
variance in order to avoid false DE calls. The technical contribution to the
uncertainty comes both from finite read-depth and the possibly ambiguous
mapping of reads to multiple transcripts.
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blasr
mapping single-molecule sequencing reads
|
Versions of package blasr |
Release | Version | Architectures |
stretch | 5.3+0-1 | amd64,arm64,mips64el,ppc64el |
buster | 5.3.2+dfsg-1.1 | amd64,arm64 |
trixie | 5.3.5+dfsg-6 | amd64,arm64,mips64el,ppc64el,riscv64 |
bookworm | 5.3.5+dfsg-6 | amd64,arm64,mips64el,ppc64el |
bullseye | 5.3.3+dfsg-5 | amd64,arm64,mips64el,ppc64el |
sid | 5.3.5+dfsg-7 | amd64,arm64,mips64el,ppc64el,riscv64 |
|
License: DFSG free
|
Basic local alignment with successive refinement (BLASR) is a method
for mapping single-molecule sequencing reads against a reference genome.
Such reads are thousands of bases long, with divergence between them
and the genome being dominated by insertion and deletion error.
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blixem
interactive browser of sequence alignments
|
Versions of package blixem |
Release | Version | Architectures |
bookworm | 4.44.1+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 4.44.1+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 4.44.1+dfsg-7.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 4.44.1+dfsg-3 | amd64,arm64,armhf,i386 |
sid | 4.44.1+dfsg-7.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
Blixem is an interactive browser of sequence alignments that have been
stacked up in a "master-slave" multiple alignment; it is not a 'true'
multiple alignment but a 'one-to-many' alignment.
- Overview section showing the positions of genes and alignments around
the alignment window
- Detail section showing the actual alignment of protein or nucleotide
sequences to the genomic DNA sequence.
- View alignments against both strands of the reference sequence.
- View sequences in nucleotide or protein mode; in protein mode, Blixem
will display the three-frame translation of the reference sequence.
- Residues are highlighted in different colours depending on whether
they are an exact match, conserved substitution or mismatch.
- Gapped alignments are supported, with insertions and deletions being
highlighted in the match sequence.
- Matches can be sorted and filtered.
- SNPs and other variations can be highlighted in the reference
sequence.
- Poly(A) tails can be displayed and poly(A) signals highlighted in the
reference sequence.
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bolt-lmm
Efficient large cohorts genome-wide Bayesian mixed-model association testing
|
Versions of package bolt-lmm |
Release | Version | Architectures |
trixie | 2.4.1+dfsg-2 | amd64,i386,ppc64el |
bookworm | 2.4.0+dfsg-1 | amd64,i386,ppc64el |
buster | 2.3.2+dfsg-3 | amd64 |
sid | 2.4.1+dfsg-2 | amd64,i386,ppc64el |
bullseye | 2.3.4+dfsg-3 | amd64,i386,ppc64el |
|
License: DFSG free
|
The BOLT-LMM software package currently consists of two main algorithms, the
BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML
algorithm for variance components analysis (i.e., partitioning of
SNP-heritability and estimation of genetic correlations).
The BOLT-LMM algorithm computes statistics for testing association between
phenotype and genotypes using a linear mixed model. By default, BOLT-LMM
assumes a Bayesian mixture-of-normals prior for the random effect attributed
to SNPs other than the one being tested. This model generalizes the standard
infinitesimal mixed model used by previous mixed model association methods,
providing an opportunity for increased power to detect associations while
controlling false positives. Additionally, BOLT-LMM applies algorithmic
advances to compute mixed model association statistics much faster than
eigendecomposition-based methods, both when using the Bayesian mixture model
and when specialized to standard mixed model association.
The BOLT-REML algorithm estimates heritability explained by genotyped SNPs and
genetic correlations among multiple traits measured on the same set of
individuals. BOLT-REML applies variance components analysis to perform these
tasks, supporting both multi-component modeling to partition SNP-heritability
and multi-trait modeling to estimate correlations. BOLT-REML applies a Monte
Carlo algorithm that is much faster than eigendecomposition-based methods for
variance components analysis at large sample sizes.
Please cite:
Po-Ru Loh, George Tucker, Brendan K Bulik-Sullivan, Bjarni J Vilhjálmsson, Hilary K Finucane, Rany M Salem, Daniel I Chasman, Paul M Ridker, Benjamin M Neale, Bonnie Berger, Nick Patterson and Alkes L Price:
Efficient Bayesian mixed-model analysis increases association power in large cohorts.
Nature Genetics
(2015)
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|
bowtie
Ultrafast memory-efficient short read aligner
|
Versions of package bowtie |
Release | Version | Architectures |
buster | 1.2.2+dfsg-4 | amd64,arm64 |
jessie | 1.1.1-2 | amd64 |
stretch | 1.1.2-6 | amd64,arm64,mips64el,ppc64el,s390x |
sid | 1.3.1-3 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
trixie | 1.3.1-3 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.3.0+dfsg1-1 | amd64,arm64,mips64el,ppc64el,s390x |
bookworm | 1.3.1-1 | amd64,arm64,mips64el,ppc64el,s390x |
Debtags of package bowtie: |
biology | nuceleic-acids |
field | biology:bioinformatics |
interface | commandline |
role | program |
science | calculation |
scope | utility |
use | analysing, comparing |
works-with | biological-sequence |
|
License: DFSG free
|
This package addresses the problem to interpret the results from the
latest (2010) DNA sequencing technologies. Those will yield fairly
short stretches and those cannot be interpreted directly. It is the
challenge for tools like Bowtie to give a chromosomal location to the
short stretches of DNA sequenced per run.
Bowtie aligns short DNA sequences (reads) to the human genome at a rate
of over 25 million 35-bp reads per hour. Bowtie indexes the genome with
a Burrows-Wheeler index to keep its memory footprint small: typically
about 2.2 GB for the human genome (2.9 GB for paired-end).
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bowtie2
ultrafast memory-efficient short read aligner
|
Versions of package bowtie2 |
Release | Version | Architectures |
buster | 2.3.4.3-1 | amd64 |
sid | 2.5.4-1 | amd64,arm64,mips64el,ppc64el,riscv64 |
jessie | 2.2.4-1 | amd64 |
trixie | 2.5.4-1 | amd64,arm64,mips64el,ppc64el,riscv64 |
bullseye | 2.4.2-2 | amd64,arm64,mips64el,ppc64el |
stretch | 2.3.0-2 | amd64 |
bookworm | 2.5.0-3 | amd64,arm64,mips64el,ppc64el |
|
License: DFSG free
|
is an ultrafast and memory-efficient tool for aligning sequencing reads
to long reference sequences. It is particularly good at aligning reads
of about 50 up to 100s or 1,000s of characters, and particularly good
at aligning to relatively long (e.g. mammalian) genomes.
Bowtie 2 indexes the genome with an FM Index to keep its memory footprint
small: for the human genome, its memory footprint is typically
around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes
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boxshade
Pretty-printing of multiple sequence alignments
|
Versions of package boxshade |
Release | Version | Architectures |
bullseye | 3.3.1-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.3.1-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 3.3.1-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 3.3.1-8 | amd64,armel,armhf,i386 |
stretch | 3.3.1-10 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 3.3.1-12 | amd64,arm64,armhf,i386 |
sid | 3.3.1-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package boxshade: |
biology | format:aln, nuceleic-acids, peptidic |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | typesetting |
works-with-format | html, plaintext, postscript, tex |
|
License: DFSG free
|
Boxshade is a program for creating good looking printouts from
multiple-aligned protein or DNA sequences. The program does not perform
the alignment by itself and requires as input a file that was created
by a multiple alignment program or manually edited with respective tools.
Boxshade reads multiple-aligned sequences from either PILEUP-MSF,
CLUSTAL-ALN, MALIGNED-data and ESEE-save files (limited to a maximum
of 150 sequences with up to 10000 elements each). Various kinds of
shading can be applied to identical/similar residues. Output is written
to screen or to a file in the following formats: ANSI/VT100, PS/EPS,
RTF, HPGL, ReGIS, LJ250-printer, ASCII, xFIG, PICT, HTML
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bppphyview
Bio++ Phylogenetic Viewer
|
Versions of package bppphyview |
Release | Version | Architectures |
bullseye | 0.6.1-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.6.1-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.6.1-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 0.3.0-1 | amd64,armel,armhf,i386 |
stretch | 0.3.0-1.1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.6.1-1 | amd64,arm64,armhf,i386 |
bookworm | 0.6.1-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package bppphyview: |
role | program |
uitoolkit | qt |
|
License: DFSG free
|
A phylogenetic tree editor developed using Bio++ and Qt. Phyview allows one
to visualize, edit, print and output phylogenetic trees and associated data.
|
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bppsuite
|
Versions of package bppsuite |
Release | Version | Architectures |
bookworm | 2.4.1-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.4.1-1 | amd64,arm64,armhf,i386 |
bullseye | 2.4.1-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.4.1-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 2.2.0-0.1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 2.4.1-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package bppsuite: |
role | program |
|
License: DFSG free
|
The Bio++ Program Suite is a package of programs using the Bio++
libraries and dedicated to Phylogenetics and Molecular Evolution. All
programs are independent, but can be combined to perform rather complex
analyses. These programs use the interface helper tools of the
libraries, and hence share the same syntax. They also have several
options in common, which may also be shared by third-party software.
The following programs are included:
- BppML for maximum likelihood analysis,
- BppSeqGen for sequences simulation,
- BppAncestor for ancestral states reconstruction,
- BppDist for distance methods,
- BppPars for parsimony analysis,
- BppSeqMan for file conversion and sequence manipulation,
- BppConsense for building consensus tree and computing
bootstrap values,
- BppReRoot for tree rerooting.
- BppTreeDraw for tree drawing.
- BppAlnScore for comparing alignments and computing alignment scores.
- BppMixedLikelihoods for computing site per site likelihoods of
components of mixture models.
- BppPopGen for population genetics analyses.
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brig
BLAST Ring Image Generator
|
Versions of package brig |
Release | Version | Architectures |
trixie | 0.95+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 0.95+dfsg-2 | amd64,arm64,armhf,i386 |
sid | 0.95+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 0.95+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.95+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.95+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
BRIG can display circular comparisons between a large number of genomes,
with a focus on handling genome assembly data.
- Images show similarity between a central reference sequence and other
sequences as concentric rings.
- BRIG will perform all BLAST comparisons and file parsing automatically
via a simple GUI.
- Contig boundaries and read coverage can be displayed for draft genomes;
customized graphs and annotations can be displayed.
- Using a user-defined set of genes as input, BRIG can display gene
presence, absence, truncation or sequence variation in a set of
complete genomes, draft genomes or even raw, unassembled sequence data.
- BRIG also accepts SAM-formatted read-mapping files enabling genomic
regions present in unassembled sequence data from multiple samples to
be compared simultaneously
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btllib-tools
Bioinformatics Technology Lab common code library tools
|
Versions of package btllib-tools |
Release | Version | Architectures |
trixie | 1.4.10+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64 |
bookworm | 1.4.10+dfsg-1 | amd64,arm64,mips64el,ppc64el |
sid | 1.4.10+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64 |
upstream | 1.7.5 |
|
License: DFSG free
|
Bioinformatics Technology Lab common code library in C++ with
Python wrappers.
This package contains the tool indexlr.
|
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busco
benchmarking sets of universal single-copy orthologs
|
Versions of package busco |
Release | Version | Architectures |
trixie | 5.5.0-3 | amd64,arm64,i386 |
sid | 5.5.0-3 | amd64,arm64,i386 |
bullseye | 5.0.0-1 | all |
bookworm | 5.4.4-1 | amd64,i386 |
|
License: DFSG free
|
Assessing genome assembly and annotation completeness with Benchmarking
Universal Single-Copy Orthologs (BUSCO).
- Automated selection of lineages issued from https://www.orthodb.org/
- Automated download of all necessary files and datasets to conduct a run
- Use prodigal for non-eukaryotic genomes
The package is enhanced by the following packages:
multiqc
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bustools
program for manipulating BUS files for single cell RNA-Seq datasets
|
Versions of package bustools |
Release | Version | Architectures |
trixie | 0.43.2+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
sid | 0.43.2+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.40.0-4 | amd64,arm64,mips64el,ppc64el,s390x |
bookworm | 0.42.0+dfsg-1 | amd64,arm64,mips64el,ppc64el,s390x |
upstream | 0.44.1 |
|
License: DFSG free
|
This package contains BUStools program, it can be used to error correct
barcodes, collapse UMIs, produce gene count or transcript compatibility
count matrices
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bwa
|
Versions of package bwa |
Release | Version | Architectures |
bullseye | 0.7.17-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.7.18-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.7.17-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 0.7.10-1 | amd64 |
stretch | 0.7.15-2+deb9u1 | amd64 |
trixie | 0.7.18-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch-backports | 0.7.17-1~bpo9+1 | amd64 |
buster | 0.7.17-3 | amd64 |
Debtags of package bwa: |
biology | nuceleic-acids, peptidic |
field | biology, biology:bioinformatics |
interface | commandline, text-mode |
role | program |
use | analysing, comparing |
|
License: DFSG free
|
BWA is a software package for mapping low-divergent sequences against
a large reference genome, such as the human genome. It consists of
three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first
algorithm is designed for Illumina sequence reads up to 100bp, while
the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM
and BWA-SW share similar features such as long-read support and split
alignment, but BWA-MEM, which is the latest, is generally recommended
for high-quality queries as it is faster and more accurate. BWA-MEM
also has better performance than BWA-backtrack for 70-100bp Illumina
reads.
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canu
single molecule sequence assembler for genomes
|
Versions of package canu |
Release | Version | Architectures |
stretch-backports | 1.7.1+dfsg-1~bpo9+1 | amd64 |
bookworm | 2.0+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.2+dfsg-5 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
buster | 1.8+dfsg-2 | amd64 |
upstream | 2.3 |
|
License: DFSG free
|
Canu is a fork of the Celera Assembler, designed for high-noise
single-molecule sequencing (such as the PacBio RS II or Oxford
Nanopore MinION).
Canu is a hierarchical assembly pipeline which runs in four steps:
- Detect overlaps in high-noise sequences using MHAP
- Generate corrected sequence consensus
- Trim corrected sequences
- Assemble trimmed corrected sequences
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|
cassiopee
index and search tool in genomic sequences
|
Versions of package cassiopee |
Release | Version | Architectures |
trixie | 1.0.9-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.0.9-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.0.5-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.9-2 | amd64,arm64,armhf,i386 |
jessie | 1.0.1+dfsg-3 | amd64,armel,armhf,i386 |
sid | 1.0.9-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.0.9-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
Cassiopee index and search library C implementation.
It is a complete rewrite of the ruby Cassiopee gem. It scans an input
genomic sequence (dna/rna/protein) and search for a subsequence with
exact match or allowing substitutions (Hamming distance) and/or
insertion/deletions.
This package contains the cassiopee and cassiopeeknife tools.
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cat-bat
taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
|
Versions of package cat-bat |
Release | Version | Architectures |
bookworm | 5.2.3-2 | amd64,arm64,ppc64el,s390x |
sid | 5.3-2 | amd64,arm64,ppc64el,riscv64,s390x |
bullseye | 5.2.2-1 | amd64,arm64,ppc64el,s390x |
trixie | 5.3-2 | amd64,arm64,ppc64el,riscv64,s390x |
upstream | 6.0.1 |
|
License: DFSG free
|
Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines
for the taxonomic classification of long DNA sequences and metagenome
assembled genomes (MAGs/bins) of both known and (highly) unknown
microorganisms, as generated by contemporary metagenomics studies. The
core algorithm of both programs involves gene calling, mapping of
predicted ORFs against the nr protein database, and voting-based
classification of the entire contig / MAG based on classification of the
individual ORFs. CAT and BAT can be run from intermediate steps if files
are formatted appropriately.
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cct
visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences
|
Versions of package cct |
Release | Version | Architectures |
trixie | 1.0.3-1 | all |
bookworm | 1.0.3-1 | all |
buster | 20170919+dfsg-1 | all |
bullseye | 1.0.0-1 | all |
stretch-backports | 20170919+dfsg-1~bpo9+1 | all |
sid | 1.0.3-1 | all |
|
License: DFSG free
|
The CGView Comparison Tool (CCT) is a package for visually comparing
bacterial, plasmid, chloroplast, or mitochondrial sequences of interest
to existing genomes or sequence collections. The comparisons are
conducted using BLAST, and the BLAST results are presented in the form
of graphical maps that can also show sequence features, gene and protein
names, COG category assignments, and sequence composition
characteristics. CCT can generate maps in a variety of sizes, including
400 Megapixel maps suitable for posters. Comparisons can be conducted
within a particular species or genus, or all available genomes can be
used. The entire map creation process, from downloading sequences to
redrawing zoomed maps, can be completed easily using scripts included
with the CCT. User-defined features or analysis results can be included
on maps, and maps can be extensively customized. To simplify program
setup, a CCT virtual machine that includes all dependencies preinstalled
is available. Detailed tutorials illustrating the use of CCT are
included with the CCT documentation.
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cd-hit
suite of programs designed to quickly group sequences
|
Versions of package cd-hit |
Release | Version | Architectures |
bookworm | 4.8.1-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 4.8.1-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 4.8.1-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 4.6.6-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 4.6.8-2 | amd64,arm64,armhf,i386 |
jessie | 4.6.1-2012-08-27-2 | amd64,armel,armhf,i386 |
sid | 4.8.1-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
cd-hit contains a number of programs designed to quickly group
sequences. cd-hit groups proteins into clusters that meet a user-defined
similarity threshold. cd-hit-est is similar to cd-hit, but designed to
group nucleotide sequences (without introns). cd-hit-est-2d is similar
to cd-hit-2d but designed to compare two nucleotide datasets. A number
of other related programs are also in this package. Please see the
cd-hit user manual, also part of this package, for further information.
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cdbfasta
Constant DataBase indexing and retrieval tools for multi-FASTA files
|
Versions of package cdbfasta |
Release | Version | Architectures |
sid | 1.00+git20230710.da8f5ba+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.00+git20230710.da8f5ba+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.00+git20181005.014498c+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.99-20100722-5 | amd64,arm64,armhf,i386 |
stretch | 0.99-20100722-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0.99-20100722-1 | amd64,armel,armhf,i386 |
bullseye | 1.00+git20181005.014498c+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
CDB (Constant DataBase) can be used for creating indices for quick
retrieval of any particular sequences from large multi-FASTA files.
It has the option to compress data records in order to save space.
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centrifuge
rapid and memory-efficient system for classification of DNA sequences
|
Versions of package centrifuge |
Release | Version | Architectures |
bookworm | 1.0.3-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el |
bullseye | 1.0.3-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el |
buster | 1.0.3-2 | amd64 |
trixie | 1.0.4.2-1 | amd64,arm64,mips64el,ppc64el,riscv64 |
sid | 1.0.4.2-1 | amd64,arm64,mips64el,ppc64el,riscv64 |
|
License: DFSG free
|
Centrifuge is a very rapid and memory-efficient system for the
classification of DNA sequences from microbial samples, with better
sensitivity than and comparable accuracy to other leading systems. The
system uses a novel indexing scheme based on the Burrows-Wheeler
transform (BWT) and the Ferragina-Manzini (FM) index, optimized
specifically for the metagenomic classification problem. Centrifuge
requires a relatively small index (e.g., 4.3 GB for ~4,100 bacterial
genomes) yet provides very fast classification speed, allowing it to
process a typical DNA sequencing run within an hour. Together these
advances enable timely and accurate analysis of large metagenomics data
sets on conventional desktop computers.
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cgview
|
Versions of package cgview |
Release | Version | Architectures |
trixie | 0.0.20100111-7 | all |
bullseye | 0.0.20100111-7 | all |
stretch | 0.0.20100111-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.0.20100111-4 | amd64,arm64,armhf,i386 |
sid | 0.0.20100111-7 | all |
bookworm | 0.0.20100111-7 | all |
|
License: DFSG free
|
CGView is a Java package for generating high quality, zoomable maps of
circular genomes. Its primary purpose is to serve as a component of
sequence annotation pipelines, as a means of generating visual output
suitable for the web. Feature information and rendering options are
supplied to the program using an XML file, a tab delimited file, or an
NCBI ptt file. CGView converts the input into a graphical map (PNG, JPG,
or Scalable Vector Graphics format), complete with labels, a title,
legends, and footnotes. In addition to the default full view map, the
program can generate a series of hyperlinked maps showing expanded
views. The linked maps can be explored using any web browser, allowing
rapid genome browsing, and facilitating data sharing. The feature labels
in maps can be hyperlinked to external resources, allowing CGView maps
to be integrated with existing web site content or databases.
In addition to the CGView application, an API is available for
generating maps from within other Java applications, using the
cgview package.
CGView can be used for any of the following:
- Bacterial genome visualization and browsing - CGView can be
incorporated into bacterial genome annotation pipelines, as a means
of generating web content for data visualization and navigation. The
PNG and image map content does not require Java applets or special
browser plugins.
- Genome poster generation - CGView can generate poster-sized images of
circular genomes in rasterized image formats or in Scalable Vector
Graphics format.
- Sequence analysis visualization - CGView can be used to display the
output of sequence analysis programs in a circular context.
CGView features:
- Images can be generated in PNG, JPG, or SVG format. See the
CGView gallery.
- Static or interactive maps can be generated. The interactive maps
make use of standard PNG images and HTML image maps. Scalable Vector
Graphics output is included in the interactive maps (see example).
- The XML input allows complete control over the appearance of the map.
- Tab delimited input files and NCBI ptt files can be used as an
alternative to the XML format.
- The CGView API can be used to incorporate CGView into Java
applications.
- The CGView applet can be used to incorporate zoomable maps into web
pages (see example).
- The CGView Server can be used to generate maps online.
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changeo
Repertoire clonal assignment toolkit (Python 3)
|
Versions of package changeo |
Release | Version | Architectures |
buster | 0.4.5-1 | all |
sid | 1.3.0-3 | all |
bookworm | 1.3.0-1 | all |
bullseye | 1.0.2-1 | all |
trixie | 1.3.0-3 | all |
|
License: DFSG free
|
Change-O is a collection of tools for processing the output of V(D)J
alignment tools, assigning clonal clusters to immunoglobulin (Ig)
sequences, and reconstructing germline sequences.
Dramatic improvements in high-throughput sequencing technologies now
enable large-scale characterization of Ig repertoires, defined as the
collection of trans-membrane antigen-receptor proteins located on the
surface of B cells and T cells. Change-O is a suite of utilities to
facilitate advanced analysis of Ig and TCR sequences following germline
segment assignment. Change-O handles output from IMGT/HighV-QUEST
and IgBLAST, and provides a wide variety of clustering methods for
assigning clonal groups to Ig sequences. Record sorting, grouping,
and various database manipulation operations are also included.
This package installs the library for Python 3.
Please cite:
Namita T. Gupta, Jason A. Vander Heiden, Mohamed Uduman, Daniel Gadala-Maria, Gur Yaari and Steven H. Kleinstein:
Link
to publication
(PubMed,eprint)
Bioinformatics
31(20):3356-3358
(2015)
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chimeraslayer
detects likely chimeras in PCR amplified DNA
|
Versions of package chimeraslayer |
Release | Version | Architectures |
jessie | 20101212+dfsg-1 | all |
sid | 20101212+dfsg1-6 | all |
trixie | 20101212+dfsg1-6 | all |
bookworm | 20101212+dfsg1-5 | all |
bullseye | 20101212+dfsg1-4 | all |
buster | 20101212+dfsg1-2 | all |
stretch | 20101212+dfsg1-1 | all |
Debtags of package chimeraslayer: |
biology | format:aln, nuceleic-acids |
field | biology, biology:molecular |
role | program |
scope | utility |
|
License: DFSG free
|
ChimeraSlayer is a chimeric sequence detection utility, compatible with
near-full length Sanger sequences and shorter 454-FLX sequences (~500bp).
Chimera Slayer involves the following series of steps that operate to
flag chimeric 16S rRNA sequences:
1. the ends of a query sequence are searched against an included
database of reference chimera-free 16S sequences to identify potential
parents of a chimera
2. candidate parents of a chimera are selected as those that form a
branched best scoring alignment to the NAST-formatted query sequence
3. the NAST alignment of the query sequence is improved in a
‘chimera-aware’ profile-based NAST realignment to the selected
reference parent sequences
4. an evolutionary framework is used to flag query sequences found to
exhibit greater sequence homology to an in silico chimera formed
between any two of the selected reference parent sequences.
To run Chimera Slayer, you need NAST-formatted sequences generated by
the nast-ier utility.
ChimeraSlayer is part of the microbiomeutil suite.
Please cite:
Brian J. Haas, Dirk Gevers, Ashlee M. Earl, Mike Feldgarden, Doyle V. Ward, Georgia Giannoukos, Dawn Ciulla, Diana Tabbaa, Sarah K. Highlander, Erica Sodergren, Barbara Methé, Todd Z. DeSantis, The Human Microbiome Consortium, Joseph F. Petrosino, Rob Knight and Bruce W. Birren:
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.
(PubMed,eprint)
Genome Research
21(3):494-504
(2011)
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chromhmm
Chromatin state discovery and characterization
|
Versions of package chromhmm |
Release | Version | Architectures |
trixie | 1.25+dfsg-1 | all |
sid | 1.25+dfsg-1 | all |
bookworm | 1.24+dfsg-1 | all |
buster | 1.18+dfsg-1 | all |
bullseye | 1.21+dfsg-1 | all |
|
License: DFSG free
|
ChromHMM is software for learning and characterizing chromatin states.
ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of
various histone modifications to discover de novo the major re-occuring
combinatorial and spatial patterns of marks. ChromHMM is based on a
multivariate Hidden Markov Model that explicitly models the presence or
absence of each chromatin mark. The resulting model can then be used to
systematically annotate a genome in one or more cell types. By automatically
computing state enrichments for large-scale functional and annotation datasets
ChromHMM facilitates the biological characterization of each state. ChromHMM
also produces files with genome-wide maps of chromatin state annotations that
can be directly visualized in a genome browser.
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chromimpute
Large-scale systematic epigenome imputation
|
Versions of package chromimpute |
Release | Version | Architectures |
bookworm | 1.0.3+dfsg-4 | all |
bullseye | 1.0.3+dfsg-2 | all |
buster | 1.0.3+dfsg-1 | all |
sid | 1.0.3+dfsg-5 | all |
trixie | 1.0.3+dfsg-5 | all |
|
License: DFSG free
|
ChromImpute takes an existing compendium of epigenomic data and uses it to
predict signal tracks for mark-sample combinations not experimentally mapped
or to generate a potentially more robust version of data sets that have been
mapped experimentally. ChromImpute bases its predictions on features from
signal tracks of other marks that have been mapped in the target sample and
the target mark in other samples with these features combined using an
ensemble of regression trees.
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cif-tools
Suite of tools to manipulate, validate and query mmCIF files
|
Versions of package cif-tools |
Release | Version | Architectures |
trixie | 1.0.12-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.0.12-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.0.0-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.0.7-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
This package contains a suite of tools for the manipulation of mmCIF files.
The structure of macro molecules is nowadays recorded in mmCIF files. Until
recently however the ancient PDB file format was used by many programs but
that format has since long been deprecated.
This package provides two tools, pdb2cif and cif2pdb, that can convert files
from one format into the other, provided that data fits of course.
Other tools are cif-validate, cif-grep, cif-diff, cif-merge and mmCQL. The
latter can be used to manipulate an mmCIF file as if it were a SQL like
database using SELECT, UPDATE, INSERT and DELETE commands.
This package depends on libcifpp.
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circlator
circularize genome assemblies
|
Versions of package circlator |
Release | Version | Architectures |
buster | 1.5.5-3 | amd64 |
stretch | 1.4.1-1 | all |
sid | 1.5.6-12 | all |
bookworm | 1.5.6-7 | amd64 |
bullseye | 1.5.6-5 | amd64 |
|
License: DFSG free
|
Circlator is a tool to automate assembly circularization for bacterial and
small eukaryotic genomes and produce accurate linear representations of
circular sequences.
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circos
plotter for visualizing data
|
Versions of package circos |
Release | Version | Architectures |
trixie | 0.69.9+dfsg-2 | all |
jessie | 0.66-1 | all |
stretch | 0.69.4+dfsg-1 | all |
buster | 0.69.6+dfsg-2 | all |
bullseye | 0.69.9+dfsg-2 | all |
bookworm | 0.69.9+dfsg-2 | all |
sid | 0.69.9+dfsg-2 | all |
Debtags of package circos: |
field | biology:bioinformatics |
role | program |
use | viewing |
|
License: DFSG free
|
Circos visualizes data in a circular layout — ideal for exploring
relationships between objects or positions, and creating highly
informative publication-quality graphics.
This package provides the Circos plotting engine, which is command-line
driven (like gnuplot) and fully scriptable.
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clearcut
extremely efficient phylogenetic tree reconstruction
|
Versions of package clearcut |
Release | Version | Architectures |
sid | 1.0.9+git20211013.b799afe-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.0.9-1 | amd64,armel,armhf,i386 |
stretch | 1.0.9-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.9-3 | amd64,arm64,armhf,i386 |
bullseye | 1.0.9-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.0.9+git20211013.b799afe-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.0.9+git20211013.b799afe-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
Clearcut is the reference implementation for the Relaxed Neighbor Joining (RNJ)
algorithm by J. Evans, L. Sheneman, and J. Foster from the Initiative
for Bioinformatics and Evolutionary Studies (IBEST) at the University of
Idaho.
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clonalframe
inference of bacterial microevolution using multilocus sequence data
|
Versions of package clonalframe |
Release | Version | Architectures |
bookworm | 1.2-11 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.2-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.2-3 | amd64,armel,armhf,i386 |
trixie | 1.2-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.2-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.2-9 | amd64,arm64,armhf,i386 |
bullseye | 1.2-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package clonalframe: |
role | program |
|
License: DFSG free
|
ClonalFrame identifies the clonal relationships between the members of
a sample, while also estimating the chromosomal position of homologous
recombination events that have disrupted the clonal inheritance.
ClonalFrame can be applied to any kind of sequence data, from a single
fragment of DNA to whole genomes. It is well suited for the analysis of
MLST data, where 7 gene fragments have been sequenced, but becomes
progressively more powerful as the sequenced regions increase in length
and number up to whole genomes. However, it requires the sequences to be
aligned. If you have genomic data that is not aligned, it is recommend to
use Mauve which produces alignment of whole bacterial genomes in
exactly the format required for analysis with ClonalFrame.
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clonalframeml
Efficient Inference of Recombination in Whole Bacterial Genomes
|
Versions of package clonalframeml |
Release | Version | Architectures |
bookworm | 1.12-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.12-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.13-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.11-3 | amd64,arm64,armhf,i386 |
trixie | 1.13-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
ClonalFrameML is a software package that performs efficient inference of
recombination in bacterial genomes. ClonalFrameML was created by Xavier
Didelot and Daniel Wilson. ClonalFrameML can be applied to any type of
aligned sequence data, but is especially aimed at analysis of whole
genome sequences. It is able to compare hundreds of whole genomes in a
matter of hours on a standard Desktop computer. There are three main
outputs from a run of ClonalFrameML: a phylogeny with branch lengths
corrected to account for recombination, an estimation of the key
parameters of the recombination process, and a genomic map of where
recombination took place for each branch of the phylogeny.
ClonalFrameML is a maximum likelihood implementation of the Bayesian
software ClonalFrame which was previously described by Didelot and
Falush (2007). The recombination model underpinning ClonalFrameML is
exactly the same as for ClonalFrame, but this new implementation is a
lot faster, is able to deal with much larger genomic dataset, and does
not suffer from MCMC convergence issues
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clonalorigin
inference of homologous recombination in bacteria using whole genome sequences
|
Versions of package clonalorigin |
Release | Version | Architectures |
trixie | 1.0-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.0-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.0-3 | amd64,arm64,armhf,i386 |
bookworm | 1.0-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.0-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
Bacteria, unlike us, can reproduce on their own. They do however have
mechanisms that transfer DNA between organisms, a process more formally
known as recombination. The mechanisms by which recombination takes
place have been studied extensively in the laboratory but much remains
to be understood concerning how, when and where recombination takes
place within natural populations of bacteria and how it helps them to
adapt to new environments. ClonalOrigin performs a comparative analysis
of the sequences of a sample of bacterial genomes in order to
reconstruct the recombination events that have taken place in their
ancestry.
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clustalo
General-purpose multiple sequence alignment program for proteins
|
Versions of package clustalo |
Release | Version | Architectures |
sid | 1.2.4-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.2.4-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.2.4-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.2.4-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.2.4-2 | amd64,arm64,armhf,i386 |
jessie | 1.2.1-1 | amd64,armel,armhf,i386 |
trixie | 1.2.4-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
Clustal Omega is a general-purpose multiple sequence alignment (MSA)
program, primarily for amino-acid sequences. It produces high quality MSAs
and is capable of handling data sets of hundreds of thousands of sequences
in reasonable time, using multiple processors where available.
Please cite:
Fabian Sievers, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding, Julie D Thompson and Desmond G Higgins:
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.
(PubMed,eprint)
Molecular Systems Biology
7:539
(2011)
Topics: Sequence analysis
|
|
clustalw
global multiple nucleotide or peptide sequence alignment
|
Versions of package clustalw |
Release | Version | Architectures |
buster | 2.1+lgpl-6 | amd64,arm64,armhf,i386 |
bookworm | 2.1+lgpl-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.1+lgpl-7 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
jessie | 2.1+lgpl-4 | amd64,armel,armhf,i386 |
sid | 2.1+lgpl-7 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
stretch | 2.1+lgpl-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.1+lgpl-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package clustalw: |
biology | format:aln, nuceleic-acids, peptidic |
field | biology, biology:bioinformatics |
interface | commandline, text-mode |
role | program |
scope | utility |
use | comparing |
works-with-format | plaintext |
|
License: DFSG free
|
This program performs an alignment of multiple nucleotide or amino acid
sequences. It recognizes the format of input sequences and whether the
sequences are nucleic acid (DNA/RNA) or amino acid (proteins). The output
format may be selected from in various formats for multiple alignments such as
Phylip or FASTA. Clustal W is very well accepted.
The output of Clustal W can be edited manually but preferably with an
alignment editor like SeaView or within its companion Clustal X. When building
a model from your alignment, this can be applied for improved database
searches. The Debian package hmmer creates such in form of an HMM.
The package is enhanced by the following packages:
clustalw-mpi
Please cite:
M. A. Larkin, G. Blackshields, N. P. Brown, R. Chenna, P. A. McGettigan, H. McWilliam, F. Valentin, I.M. Wallace, A. Wilm, R. Lopez, J. D. Thompson, T. J. Gibson and D. G. Higgins:
Clustal W and Clustal X version 2.0.
(PubMed,eprint)
Bioinformatics
23(21):2947-2948
(2007)
Topics: Sequence analysis
|
|
clustalx
Multiple alignment of nucleic acid and protein sequences (graphical interface)
|
Versions of package clustalx |
Release | Version | Architectures |
sid | 2.1+lgpl-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 2.1+lgpl-3 | amd64,armel,armhf,i386 |
stretch | 2.1+lgpl-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.1+lgpl-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.1+lgpl-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 2.1+lgpl-8 | amd64,arm64,armhf,i386 |
bullseye | 2.1+lgpl-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package clustalx: |
biology | format:aln, nuceleic-acids, peptidic |
field | biology, biology:bioinformatics |
interface | x11 |
role | program |
scope | utility |
uitoolkit | motif |
use | analysing, comparing, viewing |
works-with-format | plaintext |
x11 | application |
|
License: DFSG free
|
This package offers a GUI interface for the Clustal multiple sequence
alignment program. It provides an integrated environment for performing
multiple sequence- and profile-alignments to analyse the results.
The sequence alignment is displayed in a window on the screen.
A versatile coloring scheme has been incorporated to highlight conserved
features in the alignment. For professional presentations, one should
use the texshade LaTeX package or boxshade.
The pull-down menus at the top of the window allow you to select all the
options required for traditional multiple sequence and profile alignment.
You can cut-and-paste sequences to change the order of the alignment; you can
select a subset of sequences to be aligned; you can select a sub-range of the
alignment to be realigned and inserted back into the original alignment.
An alignment quality analysis can be performed and low-scoring segments or
exceptional residues can be highlighted.
Please cite:
M.A. Larkin, G. Blackshields, N.P. Brown, R. Chenna, P.A. McGettigan, H. McWilliam, F. Valentin, I.M. Wallace, A. Wilm, R. Lopez, J.D. Thompson, T.J. Gibson and D.G. Higgins:
Clustal W and Clustal X version 2.0.
(PubMed,eprint)
Bioinformatics
23(21):2947-2948
(2007)
Topics: Sequence analysis
|
|
cnvkit
Copy number variant detection from targeted DNA sequencing
|
Versions of package cnvkit |
Release | Version | Architectures |
bullseye | 0.9.8-1 | amd64,arm64,ppc64el |
bookworm | 0.9.9-2 | amd64,arm64,ppc64el |
sid | 0.9.10-2 | all |
experimental | 0.9.10-3~0exp0 | all |
trixie | 0.9.10-2 | all |
buster | 0.9.5-3 | amd64 |
upstream | 0.9.12 |
|
License: DFSG free
|
A command-line toolkit and Python library for detecting copy number variants
and alterations genome-wide from targeted DNA sequencing. It is designed for
use with hybrid capture, including both whole-exome and custom target panels,
and short-read sequencing platforms such as Illumina and Ion Torrent.
|
|
codonw
Correspondence Analysis of Codon Usage
|
Versions of package codonw |
Release | Version | Architectures |
bookworm | 1.4.4-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.4.4-4 | amd64,arm64,armhf,i386 |
bullseye | 1.4.4-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.4.4-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.4.4-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 1.4.4-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
CodonW is a package for codon usage analysis. It was designed to simplify
Multivariate Analysis (MVA) of codon usage. The MVA method employed in
CodonW is correspondence analysis (COA) (the most popular MVA method for
codon usage analysis). CodonW can generate a COA for codon usage, relative
synonymous codon usage or amino acid usage. Additional analyses of codon
usage include investigation of optimal codons, codon and dinucleotide bias,
and/or base composition. CodonW analyses sequences encoded by genetic codes
other than the universal code.
Topics: Sequence composition, complexity and repeats
|
|
comet-ms
Tandem mass spectrometry (MS/MS) search engine
|
Versions of package comet-ms |
Release | Version | Architectures |
bookworm | 2019015+cleaned1-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 2014022-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2019015+cleaned1-4.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 2019015+cleaned1-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2019015+cleaned1-4.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 2018012-1 | amd64,arm64,armhf,i386 |
upstream | 2021010 |
|
License: DFSG free
|
Comet is an open source tandem mass spectrometry (MS/MS) sequence
database search engine. It identifies peptides by searching MS/MS
spectra against sequences present in protein sequence databases.
This package ships a binary that does MS/MS database
searches. Supported input formats are mzXML, mzML, and ms2
files. Supported output formats are .out, SQT, and pepXML.
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concavity
predictor of protein ligand binding sites from structure and conservation
|
Versions of package concavity |
Release | Version | Architectures |
jessie | 0.1-2 | amd64,armel,armhf,i386 |
sid | 0.1+dfsg.1-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.1+dfsg.1-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.1+dfsg.1-4 | amd64,arm64,armhf,i386 |
stretch | 0.1+dfsg.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 0.1+dfsg.1-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.1+dfsg.1-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
ConCavity predicts protein ligand binding sites by combining evolutionary
sequence conservation and 3D structure.
ConCavity takes as input a PDB format protein structure and optionally
files that characterize the evolutionary sequence conservation of the chains
in the structure file.
The following result files are produced by default:
- Residue ligand binding predictions for each chain (*.scores).
- Residue ligand binding predictions in a PDB format file (residue
scores placed in the temp. factor field, *_residue.pdb).
- Pocket prediction locations in a DX format file (*.dx).
- PyMOL script to visualize the predictions (*.pml).
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conservation-code
protein sequence conservation scoring tool
|
Versions of package conservation-code |
Release | Version | Architectures |
sid | 20110309.0-8 | all |
buster | 20110309.0-7 | all |
bookworm | 20110309.0-8 | all |
stretch | 20110309.0-5 | all |
bullseye | 20110309.0-8 | all |
jessie | 20110309.0-3 | all |
trixie | 20110309.0-8 | all |
|
License: DFSG free
|
This package provides score_conservation(1), a tool to score protein sequence
conservation.
The following conservation scoring methods are implemented:
- sum of pairs
- weighted sum of pairs
- Shannon entropy
- Shannon entropy with property groupings (Mirny and Shakhnovich 1995,
Valdar and Thornton 2001)
- relative entropy with property groupings (Williamson 1995)
- von Neumann entropy (Caffrey et al 2004)
- relative entropy (Samudrala and Wang 2006)
- Jensen-Shannon divergence (Capra and Singh 2007)
A window-based extension that incorporates the estimated conservation of
sequentially adjacent residues into the score for each column is also given.
This window approach can be applied to any of the conservation scoring
methods.
The program accepts alignments in the CLUSTAL and FASTA formats.
The sequence-specific output can be used as the conservation input for
concavity.
Conservation is highly predictive in identifying catalytic sites and
residues near bound ligands.
|
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coot
model building program for macromolecular crystallography
|
Versions of package coot |
Release | Version | Architectures |
sid | 1.1.09+dfsg-2 | amd64,arm64,armhf,ppc64el |
upstream | 1.1.11 |
|
License: DFSG free
|
This is a program for constructing atomic models of macromolecules
from x-ray diffraction data. Coot displays electron density maps and
molecular models and allows model manipulations such as idealization,
refinement, manual rotation/translation, rigid-body fitting, ligand
search, solvation, mutations, rotamers. Validation tools such as
Ramachandran and geometry plots are available to the user. This
package provides a Coot build with embedded Python support.
|
|
covtobed
convert the coverage track from a BAM file into a BED file
|
Versions of package covtobed |
Release | Version | Architectures |
sid | 1.3.5+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.3.5+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.2.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.3.5+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
Reads one (or more) alignment files (sorted BAM) and prints a BED with
the coverage. It will join consecutive bases with the same coverage, and
can be used to only print a BED file with the regions having a specific
coverage range.
|
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crac
integrated RNA-Seq read analysis
|
Versions of package crac |
Release | Version | Architectures |
sid | 2.5.2+dfsg-6 | amd64,arm64,mips64el,ppc64el,riscv64 |
trixie | 2.5.2+dfsg-6 | amd64,arm64,mips64el,ppc64el,riscv64 |
bookworm | 2.5.2+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el |
bullseye | 2.5.2+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el |
stretch | 2.5.0+dfsg-1 | amd64 |
buster | 2.5.0+dfsg-3 | amd64,arm64 |
|
License: DFSG free
|
CRAC is a tool to analyze High Throughput Sequencing (HTS) data in
comparison to a reference genome. It is intended for transcriptomic
and genomic sequencing reads. More precisely, with transcriptomic
reads as input, it predicts point mutations, indels, splice junction,
and chimeric RNAs (ie, non colinear splice junctions). CRAC can also
output positions and nature of sequence error that it detects in the
reads. CRAC uses a genome index. This index must be computed before
running the read analysis. For this sake, use the command "crac-index"
on your genome files. You can then process the reads using the command
crac. See the man page of CRAC (help file) by typing "man crac". CRAC
requires large amount of main memory on your computer. For processing
against the Human genome, say 50 million reads of 100 nucleotide each,
CRAC requires about 40 gigabytes of main memory. Check whether the
system of your computing server is equipped with sufficient amount of
memory before launching an analysis.
|
|
csb
Computational Structural Biology Toolbox (CSB)
|
Versions of package csb |
Release | Version | Architectures |
trixie | 1.2.5+dfsg-10 | all |
sid | 1.2.5+dfsg-10 | all |
bookworm | 1.2.5+dfsg-8 | all |
bullseye | 1.2.5+dfsg-5 | all |
buster | 1.2.5+dfsg-3 | all |
|
License: DFSG free
|
Computational Structural Biology Toolbox (CSB) is a Python class
library for reading, storing and analyzing biomolecular structures
in a variety of formats with rich support for statistical analyses.
CSB is designed for reusability and extensibility and comes with a clean,
well-documented API following good object-oriented engineering practice.
This package contains some user executable tools.
|
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ctffind
fast and accurate defocus estimation from electron micrographs
|
Versions of package ctffind |
Release | Version | Architectures |
trixie | 4.1.14-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 4.1.14-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 5.0.2 |
|
License: DFSG free
|
This is a widely-used program for the estimation of objective lens defocus
parameters from transmission electron micrographs. Defocus parameters are
estimated by fitting a model of the microscope's contrast transfer function
(CTF) to an image's amplitude spectrum.
|
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cutadapt
Clean biological sequences from high-throughput sequencing reads
|
Versions of package cutadapt |
Release | Version | Architectures |
bullseye | 3.2-2 | all |
trixie | 4.7-2 | all |
stretch | 1.12-2 | all |
sid | 4.7-2 | all |
bookworm | 4.2-1 | all |
buster | 1.18-1 | all |
upstream | 5.0 |
|
License: DFSG free
|
Cutadapt helps with biological sequence clean tasks by finding the adapter
or primer sequences in an error-tolerant way.
It can also modify and filter reads in various ways.
Adapter sequences can contain IUPAC wildcard characters.
Also, paired-end reads and even colorspace data is supported.
If you want, you can also just demultiplex your input data, without removing
adapter sequences at all.
This package contains the user interface.
The package is enhanced by the following packages:
multiqc
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cutesv
comprehensive discovery of structural variations of genomic sequences
|
Versions of package cutesv |
Release | Version | Architectures |
sid | 2.1.1-1 | all |
bookworm | 2.0.2-1 | all |
trixie | 2.1.1-1 | all |
|
License: DFSG free
|
Long-read sequencing enables the comprehensive discovery of structural
variations (SVs). However, it is still non-trivial to achieve high
sensitivity and performance simultaneously due to the complex SV
characteristics implied by noisy long reads.
cuteSV is a sensitive, fast and scalable long-read-based SV detection
approach. cuteSV uses tailored methods to collect the signatures of
various types of SVs and employs a clustering-and-refinement method to
analyze the signatures to implement sensitive SV detection. Benchmarks
on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology
(ONT) datasets demonstrate that cuteSV has better yields and scalability
than state-of-the-art tools.
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daligner
local alignment discovery between long nucleotide sequencing reads
|
Versions of package daligner |
Release | Version | Architectures |
bullseye | 1.0+git20200727.ed40ce5-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.0+git20240119.335105d-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.0+git20240119.335105d-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.0+git20221215.bd26967-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.0+20161119-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.0+git20180524.fd21879-1 | amd64,arm64,armhf,i386 |
|
License: DFSG free
|
These tools permit one to find all significant local alignments between
reads encoded in a Dazzler database. The assumption is that the reads are
from a Pacific Biosciences RS II long read sequencer. That is, the reads
are long and noisy, up to 15% on average.
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damapper
long read to reference genome mapping tool
|
Versions of package damapper |
Release | Version | Architectures |
trixie | 0.0+git20240314.b025cf9-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.0+git20210330.ab45103-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.0+git20200322.b2c9d7f-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.0+git20240314.b025cf9-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
Recognised as the Damapper Library, this is a long read to reference
genome mapping command line tool.
For a given reference database 'X' and read block 'Y', damapper produces
the single file 'Y.X.las'. Each output file is sorted in order of the
A-reads, and if a match is a chain of local alignments, then the LA's in
the chain occur in increasing order of A-coordinates.
HPC.damapper writes a UNIX shell script to the standard output that maps
every read in blocks to of database to a
reference sequence [. If is missing then only the single
block is mapped, and if is also missing then all blocks
of the database are mapped.]
This package contains the damapper and HPC.damapper binaries.
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datamash
statistics tool for command-line interface
|
Versions of package datamash |
Release | Version | Architectures |
stretch | 1.0.7-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 1.8-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.0.6-2 | amd64,armel,armhf,i386 |
bookworm | 1.7-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.8-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.7-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.4-1 | amd64,arm64,armhf,i386 |
|
License: DFSG free
|
GNU Datamash is a command-line program which performs basic numeric,
textual and statistical operations on input textual data files. It is
designed to be portable and reliable, and aid researchers to easily
automate analysis pipelines, without writing code or even short scripts.
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dawg
simulate the evolution of recombinant DNA sequences
|
Versions of package dawg |
Release | Version | Architectures |
stretch | 1.2-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.2-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.2-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.2-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.2-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.2-2 | amd64,arm64,armhf,i386 |
|
License: DFSG free
|
DNA Assembly with Gaps (Dawg) is an application designed to simulate the
evolution of recombinant DNA sequences in continuous time based on the robust
general time reversible model with gamma and invariant rate heterogeneity and
a novel length-dependent model of gap formation. The application accepts
phylogenies in Newick format and can return the sequence of any node,
allowing for the exact evolutionary history to be recorded at the discretion
of users. Dawg records the gap history of every lineage to produce the true
alignment in the output. Many options are available to allow users to
customize their simulations and results.
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dazzdb
manage nucleotide sequencing read data
|
Versions of package dazzdb |
Release | Version | Architectures |
bullseye | 1.0+git20201103.8d98c37-1+deb11u1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.0+20161112-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.0+git20180908.0bd5e07-1 | amd64,arm64,armhf,i386 |
sid | 1.0+git20240115.be65e59-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.0+git20240115.be65e59-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.0+git20221215.aad3a46-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
To facilitate the multiple phases of the dazzler assembler, all the read data
is organized into what is effectively a database of the
reads and their meta-information. The design goals for this data base
are as follows:
- The database stores the source Pacbio read information in such a
way that it can re-create the original input data, thus permitting
a user to remove the (effectively redundant) source files. This
avoids duplicating the same data, once in the source file and once
in the database.
- The data base can be built up incrementally, that is new sequence
data can be added to the data base over time.
- The data base flexibly allows one to store any meta-data desired for
reads. This is accomplished with the concept of tracks that
implementors can add as they need them.
- The data is held in a compressed form equivalent to the .dexta and
.dexqv files of the data extraction module. Both the .fasta and
.quiva information for each read is held in the data base and can be
recreated from it. The .quiva information can be added separately and
later on if desired.
- To facilitate job parallel, cluster operation of the phases of the
assembler, the database has a concept of a current partitioning in
which all the reads that are over a given length and optionally
unique to a well, are divided up into blocks containing roughly a
given number of bases, except possibly the last block which may have
a short count. Often programs can be run on blocks or pairs of blocks
and each such job is reasonably well balanced as the blocks are all
the same size. One must be careful about changing the partition
during an assembly as doing so can void the structural validity of
any interim block-based results.
|
|
deblur
deconvolution for Illumina amplicon sequencing
|
Versions of package deblur |
Release | Version | Architectures |
sid | 1.1.1-3 | all |
trixie | 1.1.1-3 | all |
|
License: DFSG free
|
Deblur is a greedy deconvolution algorithm for amplicon sequencing
based on Illumina Miseq/Hiseq error profiles. The authors recommend
using Deblur via the QIIME2 plugin q2-deblur. Examples of its use can be
found within the plugin itself. However, Deblur itself does not depend
on QIIME2.
The input to Deblur workflow is a directory of FASTA or FASTQ files
(1 per sample) or a single demultiplexed FASTA or FASTQ file. These
files can be gzip'd. The output directory will contain three BIOM
tables in which the observation IDs are the Deblurred sequences. The
outputs are contingent on the reference databases used and a more
focused discussion on them is in the subsequent README section titled
"Positive and Negative Filtering." The output files are as follows:
-
reference-hit.biom : contains only Deblurred reads matching the
positive filtering database. By default, a reference composed of 16S
sequences is used, and this resulting table will contain only those
reads which recruit at a coarse level to it will be retained. Reads
are also filtered against the negative reference, which by default
will remove any read which appears to be PhiX or adapter.
-
reference-hit.seqs.fa : a fasta file containing all the sequences
in reference-hit.biom
-
reference-non-hit.biom : contains only Deblurred reads that did not
align to the positive filtering database. Negative filtering is also
appied to this table, so by default, PhiX and adapter are removed.
-
reference-non-hit.seqs.fa : a fasta file containing all the
sequences in reference-non-hit.biom
-
all.biom : contains all Deblurred reads. This file represents the
union of the "reference-hit.biom" and "reference-non-hit.biom" tables.
-
all.seqs.fa : a fasta file containing all the sequences in all.biom
Deblur uses two types of filtering on the sequences:
-
Negative mode - removes known artifact sequences (i.e. sequences
aligning to PhiX or Adapter with >=95% identity and coverage).
-
Positive mode - keeps only sequences similar to a reference database
(by default known 16S sequences). SortMeRNA is used, and any sequence
with an e-value <= 10 is retained. Deblur also outputs a BIOM table
without this positive filtering step (named all.biom).
The FASTA files for both of these filtering steps can be supplied via
the --neg-ref-fp and --pos-ref-fp options. By default, the negative
database is composed of PhiX and adapter sequence and the positive
database of known 16S sequences.
Deblur uses negative mode filtering to remove known artifact (i.e. PhiX
and Adapter sequences) prior to denoising. The output of Deblur contains
three files: all.biom, which includes all sOTUs, reference-hit.biom,
which contains the output of positive filtering of the sOTUs (default
only sOTUs similar to 16S sequences), and reference-non-hit.biom,
which contains only sOTUs failing the positive filtering (default only
non-16S sOTUs).
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|
deepnano
alternative basecaller for MinION reads of genomic sequences
|
Versions of package deepnano |
Release | Version | Architectures |
bullseye | 0.0+git20170813.e8a621e-3.1 | amd64,arm64,armhf,i386,ppc64el,s390x |
buster | 0.0+git20170813.e8a621e-3 | amd64,arm64,i386 |
|
License: DFSG free
|
DeepNano is alternative basecaller for Oxford Nanopore MinION reads
based on deep recurrent neural networks.
Currently it works with SQK-MAP-006 and SQK-MAP-005 chemistry and as a
postprocessor for Metrichor.
|
|
delly
Structural variant discovery by read analysis
|
Versions of package delly |
Release | Version | Architectures |
bullseye | 0.8.7-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.1.8-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.1.8-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 0.8.1-2 | amd64,arm64,armhf |
bookworm | 1.1.6-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 1.3.2 |
|
License: DFSG free
|
Delly performs Structural variant discovery by integrated paired-end and
split-read analysis. It discovers, genotypes and visualizes deletions,
tandem duplications, inversions and translocations at single-nucleotide
resolution in short-read massively parallel sequencing data. It uses
paired-ends, split-reads and read-depth to sensitively and accurately
delineate genomic rearrangements throughout the genome.
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density-fitness
Calculates per-residue electron density scores
|
Versions of package density-fitness |
Release | Version | Architectures |
trixie | 1.0.12-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.0.12-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.0.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.0.8-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
The program density-fitness calculates electron density metrics,
for main- (includes Cβ atom) and side-chain atoms of individual residues.
For this calculation, the program uses the structure model in either PDB
or mmCIF format and the electron density from the 2mFo-DFc and mFo-DFc maps.
If these maps are not readily available, the MTZ file and model can be used
to calculate maps clipper. Density-fitness support both X-ray and electron
diffraction data.
This program is essentially a reimplementation of edstats, a program
available from the CCP4 suite. However, the output now contains only the
RSR, SRSR and RSCC fields as in edstats with the addition of EDIAm
and OPIA and no longer requires pre-calculated map coefficients.
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|
dextractor
(d)extractor and compression command library
|
|
License: DFSG free
|
Dextractor commands allow one to pull exactly and only the
information needed for assembly and reconstruction from the source HDF5
files produced by the PacBio RS II sequencer, or from the source BAM
files produced by the PacBio Sequel sequencer.
For each of the three extracted file types -- fasta, quiva, and
arrow -- the library contains commands to compress the given file
type, and to decompress it, which is a reversible process delivering
the original uncompressed file. The compressed .fasta files, with the
extension .dexta, consume 1/4 byte per base. The compressed .quiva
files, with the extension .dexqv, consume 1.5 bytes per base on
average, and the compressed .arrow files, with the extension .dexar,
consume 1/4 byte per base
For more information, please view the available documentation at
https://github.com/thegenemyers/DEXTRACTOR
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|
dialign
Segment-based multiple sequence alignment
|
Versions of package dialign |
Release | Version | Architectures |
buster | 2.2.1-10 | amd64,arm64,armhf,i386 |
sid | 2.2.1-13 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 2.2.1-13 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.2.1-11 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.2.1-11 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 2.2.1-7 | amd64,armel,armhf,i386 |
stretch | 2.2.1-8 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package dialign: |
biology | format:aln, nuceleic-acids, peptidic |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing, comparing |
works-with-format | plaintext |
|
License: DFSG free
|
DIALIGN2 is a command line tool to perform multiple alignment of
protein or DNA sequences. It constructs alignments from gapfree pairs
of similar segments of the sequences. This scoring scheme for
alignments is the basic difference between DIALIGN and other global or
local alignment methods. Note that DIALIGN does not employ any kind of
gap penalty.
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dialign-tx
Segment-based multiple sequence alignment
|
Versions of package dialign-tx |
Release | Version | Architectures |
bookworm | 1.0.2-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.0.2-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.0.2-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.0.2-7 | amd64,armel,armhf,i386 |
bullseye | 1.0.2-13 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.2-12 | amd64,arm64,armhf,i386 |
stretch | 1.0.2-9 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package dialign-tx: |
field | biology, biology:bioinformatics |
role | program |
scope | utility |
use | comparing |
works-with-format | plaintext |
|
License: DFSG free
|
DIALIGN-TX is a command line tool to perform multiple alignment of protein or
DNA sequences. It is a complete reimplementation of the segment-base approach
including several new improvements and heuristics that significantly enhance
the quality of the output alignments compared to DIALIGN 2.2 and DIALIGN-T.
For pairwise alignment, DIALIGN-TX uses a fragment-chaining algorithm that
favours chains of low-scoring local alignments over isolated high-scoring
fragments. For multiple alignment, DIALIGN-TX uses an improved greedy
procedure that is less sensitive to spurious local sequence similarities.
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diamond-aligner
accelerated BLAST compatible local sequence aligner
|
Versions of package diamond-aligner |
Release | Version | Architectures |
trixie | 2.1.9-1 | amd64,arm64,ppc64el,riscv64,s390x |
sid | 2.1.9-1 | amd64,arm64,ppc64el,riscv64,s390x |
bookworm | 2.1.3-1 | amd64,arm64,ppc64el,s390x |
bullseye | 2.0.7-1 | amd64,arm64,ppc64el,s390x |
buster | 0.9.24+dfsg-1 | amd64 |
stretch-backports | 0.9.22+dfsg-2~bpo9+1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
upstream | 2.1.10 |
|
License: DFSG free
|
DIAMOND is a sequence aligner for protein and translated DNA searches
and functions as a drop-in replacement for the NCBI BLAST software
tools. It is suitable for protein-protein search as well as DNA-protein
search on short reads and longer sequences including contigs and
assemblies, providing a speedup of BLAST ranging up to x20,000.
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discosnp
discovering Single Nucleotide Polymorphism from raw set(s) of reads
|
Versions of package discosnp |
Release | Version | Architectures |
buster | 2.3.0-2 | amd64,arm64,i386 |
jessie | 1.2.5-1 | amd64,armel,armhf,i386 |
bookworm | 2.6.2-2 | amd64,arm64,mips64el,ppc64el |
trixie | 2.6.2-4 | amd64,arm64,mips64el,ppc64el,riscv64 |
sid | 2.6.2-4 | amd64,arm64,mips64el,ppc64el,riscv64 |
stretch | 1.2.6-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 4.4.4-1 | amd64,arm64,i386,mips64el,ppc64el,s390x |
|
License: DFSG free
|
Software discoSnp is designed for discovering Single Nucleotide
Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation
Sequencers (NGS).
Note that number of input read sets is not constrained, it can be one, two,
or more. Note also that no other data as reference genome or annotations
are needed.
The software is composed by two modules. First module, kissnp2, detects SNPs
from read sets. A second module, kissreads, enhance the kissnp2 results by
computing per read set and for each found SNP:
1) its mean read coverage
2) the (phred) quality of reads generating the polymorphism.
This program is superseded by DiscoSnp++.
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disulfinder
cysteines disulfide bonding state and connectivity predictor
|
Versions of package disulfinder |
Release | Version | Architectures |
sid | 1.2.11-12 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.2.11-8 | amd64,arm64,armhf,i386 |
bullseye | 1.2.11-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.2.11-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.2.11-4 | amd64,armel,armhf,i386 |
trixie | 1.2.11-12 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.2.11-12 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package disulfinder: |
role | program |
|
License: DFSG free
|
'disulfinder' is for predicting the disulfide bonding state of cysteines
and their disulfide connectivity starting from sequence alone. Disulfide
bridges play a major role in the stabilization of the folding process for
several proteins. Prediction of disulfide bridges from sequence alone is
therefore useful for the study of structural and functional properties
of specific proteins. In addition, knowledge about the disulfide bonding
state of cysteines may help the experimental structure determination
process and may be useful in other genomic annotation tasks.
'disulfinder' predicts disulfide patterns in two computational stages:
(1) the disulfide bonding state of each cysteine is predicted by a
BRNN-SVM binary classifier; (2) cysteines that are known to participate
in the formation of bridges are paired by a Recursive Neural Network
to obtain a connectivity pattern.
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dnaclust
tool for clustering millions of short DNA sequences
|
Versions of package dnaclust |
Release | Version | Architectures |
sid | 3-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 3-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 3-6 | amd64,arm64,armhf,i386 |
bullseye | 3-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 3-2 | amd64,armel,armhf,i386 |
bookworm | 3-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 3-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
dnaclust is a tool for clustering large number of short DNA sequences.
The clusters are created in such a way that the "radius" of each
clusters is no more than the specified threshold.
The input sequences to be clustered should be in Fasta format. The id
of each sequence is based on the first word of the seqeunce in the Fasta
format. The first word is the prefix of the header up to the first
occurrence of white space characters in the header.
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dnarrange
Method to find rearrangements in long DNA reads relative to a genome seq
|
Versions of package dnarrange |
Release | Version | Architectures |
trixie | 1.5.3-1 | all |
bookworm | 1.5.3-1 | all |
sid | 1.5.3-1 | all |
upstream | 1.6.2 |
|
License: DFSG free
|
This package provides utilities to align the reads
to the genome, find rearrangements and draw pictures of rearranged groups
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dotter
detailed comparison of two genomic sequences
|
Versions of package dotter |
Release | Version | Architectures |
bullseye | 4.44.1+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 4.44.1+dfsg-7.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 4.44.1+dfsg-7.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 4.44.1+dfsg-3 | amd64,arm64,armhf,i386 |
bookworm | 4.44.1+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
Dotter is a graphical dot-matrix program for detailed comparison of two
sequences.
- Every residue in one sequence is compared to every residue in the
other, and a matrix of scores is calculated.
- One sequence is plotted on the x-axis and the other on the y-axis.
- Noise is filtered out so that alignments appear as diagonal lines.
- Pairwise scores are averaged over a sliding window to make the score
matrix more intelligible.
- The averaged score matrix forms a three-dimensional landscape,
with the two sequences in two dimensions and the height of the
peaks in the third. This landscape is projected onto two
dimensions using a grey-scale image - the darker grey of a peak,
the higher the score is.
- The contrast and threshold of the grey-scale image can be adjusted
interactively, without having to recalculate the score matrix.
- An Alignment Tool is provided to examine the sequence alignment that
the grey-scale image represents.
- Known high-scoring pairs can be loaded from a GFF file and overlaid
onto the plot.
- Gene models can be loaded from GFF and displayed alongside the
relevant axis.
- Compare a sequence against itself to find internal repeats.
- Find overlaps between multiple sequences by making a dot-plot of all
sequences versus themselves.
- Run Dotter in batch mode to create large, time-consuming dot-plots as
a background process.
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drop-seq-tools
|
Versions of package drop-seq-tools |
Release | Version | Architectures |
bookworm | 2.5.2+dfsg-1 | all |
bullseye | 2.4.0+dfsg-6 | all |
trixie | 3.0.2+dfsg-1 | all |
sid | 3.0.2+dfsg-1 | all |
|
License: DFSG free
|
This software provide for core computational analysis of Drop-seq data,
which shows you how to transform raw sequence data into an expression
measurement for each gene in each individual cell.
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dssp
protein secondary structure assignment based on 3D structure
|
Versions of package dssp |
Release | Version | Architectures |
trixie | 4.4.10-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 4.4.10-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 4.0.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 4.2.2-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 2.2.1-2 | amd64,armel,armhf,i386 |
buster | 3.0.0-3 | amd64,arm64,armhf,i386 |
stretch | 2.2.1-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
DSSP is an application you use to assign the secondary structure of a protein
based on its solved three dimensional (3D) structure.
This version (4.2) of DSSP is a rewrite that writes annotated mmCIF files
by default but can still produce the older dssp format. New is also the
support of PP helices.
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dwgsim
short sequencing read simulator
|
Versions of package dwgsim |
Release | Version | Architectures |
buster | 0.1.12-2 | amd64,arm64,armhf |
stretch | 0.1.11-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 0.1.14-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.1.14-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.1.14-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.1.12-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
DWGSIM simulates short sequencing reads from modern sequencing platforms.
DWGSIM generates base error rates using a parametric model, allowing a more
realisic error profile. It was originally developed for use in evaluating
short read aligners.
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e-mem
Efficient computation of Maximal Exact Matches for very large genomes
|
Versions of package e-mem |
Release | Version | Architectures |
bullseye | 1.0.1-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.0.1-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.0.1-2 | amd64,arm64,armhf,i386 |
bookworm | 1.0.1-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.0.1-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
E-MEM enables efficient computation of Maximal Exact Matches (MEMs) that
does not use full text indexes. The algorithm uses much less space and
is highly amenable to parallelization. It can compute all MEMs of
minimum length 100 between the whole human and mouse genomes on a 12
core machine in 10 min and 2 GB of memory; the required memory can be as
low as 600 MB. It can run efficiently genomes of any size. Extensive
testing and comparison with currently best algorithms is provided.
Mummer has many different scripts where one of the key program is MEM
computation. In all the scripts, the MEM computation program can be
replaced with e-mem with ease for better performance.
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ea-utils
command-line tools for processing biological sequencing data
|
Versions of package ea-utils |
Release | Version | Architectures |
stretch | 1.1.2+dfsg-4 | amd64,arm64,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.1.2+dfsg-6 | amd64,arm64,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.1.2+dfsg-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.1.2+dfsg-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.1.2+dfsg-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.1.2+dfsg-5 | amd64,arm64,armhf,i386 |
|
License: DFSG free
|
Ea-utils provides a set of command-line tools for processing biological
sequencing data, barcode demultiplexing, adapter trimming, etc.
Primarily written to support an Illumina based pipeline - but should work with
any FASTQs.
Main Tools are:
-
fastq-mcf
Scans a sequence file for adapters, and, based on a log-scaled threshold,
determines a set of clipping parameters and performs clipping. Also does
skewing detection and quality filtering.
-
fastq-multx
Demultiplexes a fastq. Capable of auto-determining barcode id's based on a
master set fields. Keeps multiple reads in-sync during demultiplexing. Can
verify that the reads are in-sync as well, and fail if they're not.
-
fastq-join
Similar to audy's stitch program, but in C, more efficient and supports some
automatic benchmarking and tuning. It uses the same "squared distance for
anchored alignment" as other tools.
-
varcall
Takes a pileup and calculates variants in a more easily parameterized manner
than some other tools.
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ecopcr
estimate PCR barcode primers quality
|
Versions of package ecopcr |
Release | Version | Architectures |
stretch | 0.5.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.0.1+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.0.1+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.0.1+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.0.1+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.0.1+dfsg-1 | amd64,arm64,armhf,i386 |
|
License: DFSG free
|
DNA barcoding is a tool for characterizing the species origin using a
short sequence from a standard position and agreed upon position in the
genome. To be used as a DNA barcode, a genome locus should vary among
individuals of the same species only to a minor degree and it should
vary among species very quickly. From a practical point of view, a
barcode locus should be flanked by two conserved regions to design PCR
primers. Several manually discovered barcode loci like COI, rbcL, 18S,
16S and 23S rDNA, or trnH-ps are routinely used today, but no objective
function has been described to measure their quality in terms of
universality (barcode coverage, Bc ) or in terms of taxonomical
discrimination capacity (barcode specificity, Bs ).
ecoPCR is an electronic PCR software developed by LECA and
Helix-Project. It helps to estimate Barcode primers quality. In
conjunction with OBITools you can postprocess ecoPCR output to compute
barcode coverage and barcode specificity. New barcode primers can be
developed using the ecoPrimers software
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|
edtsurf
triangulated mesh surfaces for protein structures
|
Versions of package edtsurf |
Release | Version | Architectures |
stretch | 0.2009-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 0.2009-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 0.2009-3 | amd64,armel,armhf,i386 |
bookworm | 0.2009-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.2009-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.2009-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 0.2009-6 | amd64,arm64,armhf,i386 |
|
License: DFSG free
|
EDTSurf is a open source program to construct triangulated surfaces
for macromolecules. It generates three major macromolecular surfaces:
van der Waals surface, solvent-accessible surface and molecular surface
(solvent-excluded surface). EDTsurf also identifies cavities which are
inside of macromolecules.
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eigensoft
reduction of population bias for genetic analyses
|
Versions of package eigensoft |
Release | Version | Architectures |
sid | 8.0.0+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 6.1.4+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 7.2.1+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 8.0.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 8.0.0+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 7.2.1+dfsg-1 | amd64,arm64,armhf,i386 |
|
License: DFSG free
|
The EIGENSOFT package combines functionality from the group's population
genetics methods (Patterson et al. 2006) and their EIGENSTRAT stratification
method (Price et al. 2006). The EIGENSTRAT method uses principal components
analysis to explicitly model ancestry differences between cases and
controls along continuous axes of variation; the resulting correction is
specific to a candidate marker's variation in frequency across ancestral
populations, minimizing spurious associations while maximizing power to
detect true associations. The EIGENSOFT package has a built-in plotting
script and supports multiple file formats and quantitative phenotypes.
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elph
DNA/protein sequence motif finder
|
Versions of package elph |
Release | Version | Architectures |
trixie | 1.0.1-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.0.1-2 | amd64,arm64,armhf,i386 |
sid | 1.0.1-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.0.1-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.0.1-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
ELPH (Estimated Locations of Pattern Hits) is a general-purpose
Gibbs sampler for finding motifs in a set of DNA or protein sequences.
The program takes as input a set containing anywhere from a few dozen to
thousands of sequences, and searches through them for the most common
motif, assuming that each sequence contains one copy of the motif. ELPH
was used to find patterns such as ribosome binding sites (RBSs) and exon
splicing enhancers (ESEs).
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embassy-domainatrix
Extra EMBOSS commands to handle domain classification file
|
Versions of package embassy-domainatrix |
Release | Version | Architectures |
stretch | 0.1.660-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0.1.650-1 | amd64,armel,armhf,i386 |
trixie | 0.1.660-5 | amd64,arm64,mips64el,ppc64el,riscv64 |
bookworm | 0.1.660-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.1.660-3 | amd64,arm64,armhf,i386 |
bullseye | 0.1.660-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.1.660-5 | amd64,arm64,mips64el,ppc64el,riscv64 |
Debtags of package embassy-domainatrix: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing, converting, editing, searching |
works-with-format | plaintext |
|
License: DFSG free
|
The DOMAINATRIX programs were developed by Jon Ison and colleagues at MRC HGMP
for their protein domain research. They are included as an EMBASSY package as
a work in progress.
Applications in the current domainatrix release are cathparse (generates DCF
file from raw CATH files), domainnr (removes redundant domains from a DCF
file), domainreso (removes low resolution domains from a DCF file), domainseqs
(adds sequence records to a DCF file), domainsse (adds secondary structure
records to a DCF file), scopparse (generates DCF file from raw SCOP files) and
ssematch (searches a DCF file for secondary structure matches).
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embassy-domalign
Extra EMBOSS commands for protein domain alignment
|
Versions of package embassy-domalign |
Release | Version | Architectures |
bookworm | 0.1.660-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 0.1.650-1 | amd64,armel,armhf,i386 |
trixie | 0.1.660-5 | amd64,arm64,mips64el,ppc64el,riscv64 |
stretch | 0.1.660-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 0.1.660-5 | amd64,arm64,mips64el,ppc64el,riscv64 |
buster | 0.1.660-3 | amd64,arm64,armhf,i386 |
bullseye | 0.1.660-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package embassy-domalign: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing, comparing, editing |
works-with-format | plaintext |
|
License: DFSG free
|
The DOMALIGN programs were developed by Jon Ison and colleagues at MRC HGMP
for their protein domain research. They are included as an EMBASSY package as
a work in progress.
Applications in the current domalign release are allversusall (sequence
similarity data from all-versus-all comparison), domainalign (generates
alignments (DAF file) for nodes in a DCF file), domainrep (reorders DCF file
to identify representative structures) and seqalign (extend alignments (DAF
file) with sequences (DHF file)).
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embassy-domsearch
Extra EMBOSS commands to search for protein domains
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Versions of package embassy-domsearch |
Release | Version | Architectures |
sid | 0.1.660-4 | amd64,arm64,mips64el,ppc64el,riscv64 |
buster | 0.1.660-3 | amd64,arm64,armhf,i386 |
bullseye | 0.1.660-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.1.660-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 0.1.660-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 0.1.660-4 | amd64,arm64,mips64el,ppc64el,riscv64 |
jessie | 0.1.650-1 | amd64,armel,armhf,i386 |
Debtags of package embassy-domsearch: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing |
|
License: DFSG free
|
The DOMSEARCH programs were developed by Jon Ison and colleagues at MRC HGMP
for their protein domain research. They are included as an EMBASSY package as
a work in progress.
Applications in this DOMSEARCH release are seqfraggle (removes fragment
sequences from DHF files), seqnr (removes redundancy from DHF files), seqsearch
(generates PSI-BLAST hits (DHF file) from a DAF file), seqsort (Remove
ambiguous classified sequences from DHF files) and seqwords (Generates DHF
files from keyword search of UniProt).
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emboss
European molecular biology open software suite
|
Versions of package emboss |
Release | Version | Architectures |
sid | 6.6.0+dfsg-15 | amd64,arm64,mips64el,ppc64el,riscv64 |
stretch | 6.6.0+dfsg-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 6.6.0+dfsg-7 | amd64,arm64,armhf,i386 |
bullseye | 6.6.0+dfsg-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 6.6.0+dfsg-12 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 6.6.0+dfsg-15 | amd64,arm64,mips64el,ppc64el,riscv64 |
jessie | 6.6.0+dfsg-1 | amd64,armel,armhf,i386 |
Debtags of package emboss: |
field | biology, biology:bioinformatics, biology:molecular |
interface | commandline |
role | program |
scope | suite |
use | analysing, comparing, converting, editing, organizing, searching, text-formatting, typesetting, viewing |
works-with | db |
works-with-format | plaintext |
|
License: DFSG free
|
EMBOSS is a free Open Source software analysis package specially developed for
the needs of the molecular biology (e.g. EMBnet) user community. The software
automatically copes with data in a variety of formats and even allows
transparent retrieval of sequence data from the web. Also, as extensive
libraries are provided with the package, it is a platform to allow other
scientists to develop and release software in true open source spirit. EMBOSS
also integrates a range of currently available packages and tools for sequence
analysis into a seamless whole. EMBOSS breaks the historical trend towards
commercial software packages.
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emmax
genetic mapping considering population structure
|
Versions of package emmax |
Release | Version | Architectures |
sid | 0~beta.20100307-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0~beta.20100307-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0~beta.20100307-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0~beta.20100307-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
EMMAX is a statistical test for large scale human or model organism
association mapping accounting for the sample structure. In addition
to the computational efficiency obtained by EMMA algorithm, EMMAX takes
advantage of the fact that each locus explains only a small fraction of
complex traits, which allows one to avoid repetitive variance component
estimation procedure, resulting in a significant amount of increase in
computational time of association mapping using mixed model.
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estscan
ORF-independent detector of coding DNA sequences
|
Versions of package estscan |
Release | Version | Architectures |
bullseye | 3.0.3-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 3.0.3-3 | amd64,arm64,armhf,i386 |
bookworm | 3.0.3-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 3.0.3-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 3.0.3-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
ESTScan is a program that can detect coding regions in DNA sequences,
even if they are of low quality. ESTScan will also detect and correct
sequencing errors that lead to frameshifts. ESTScan is not a gene
prediction program , nor is it an open reading frame detector. In fact,
its strength lies in the fact that it does not require an open reading
frame to detect a coding region. As a result, the program may miss a
few translated amino acids at either the N or the C terminus, but will
detect coding regions with high selectivity and sensitivity.
ESTScan takes advantages of the bias in hexanucleotide usage found in
coding regions relative to non-coding regions. This bias is formalized
as an inhomogeneous 3-periodic fifth-order Hidden Markov Model
(HMM). Additionally, the HMM of ESTScan has been extended to allows
insertions and deletions when these improve the coding region statistics.
Please cite:
C. Lottaz, C. Iseli, CV. Jongeneel and Philipp Bucher:
Modeling sequencing errors by combining Hidden Markov models
Bioinformatics
19:103-112
(2003)
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examl
Exascale Maximum Likelihood (ExaML) code for phylogenetic inference
|
Versions of package examl |
Release | Version | Architectures |
bookworm | 3.0.22-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 3.0.22-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 3.0.22-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 3.0.22-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 3.0.21-2 | amd64,i386 |
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License: DFSG free
|
Exascale Maximum Likelihood (ExaML) is a code for phylogenetic inference
using MPI. This code implements the popular RAxML search algorithm for
maximum likelihood based inference of phylogenetic trees.
ExaML is a strapped-down light-weight version of RAxML for phylogenetic
inference on huge datasets. It can only execute some very basic
functions and is intended for computer-savvy users that can write little
perl-scripts and have experience using queue submission scripts for
clusters. ExaML only implements the CAT and GAMMA models of rate
heterogeneity for binary, DNA, and protein data.
ExaML uses a radically new MPI parallelization approach that yields
improved parallel efficiency, in particular on partitioned multi-gene or
whole-genome datasets. It also implements a new load balancing algorithm
that yields better parallel efficiency.
It is up to 4 times faster than its predecessor RAxML-Light and scales
to a larger number of processors.
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exonerate
generic tool for pairwise sequence comparison
|
Versions of package exonerate |
Release | Version | Architectures |
jessie | 2.2.0-6 | amd64,armel,armhf,i386 |
sid | 2.4.0-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 2.4.0-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 2.4.0-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.4.0-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.4.0-4 | amd64,arm64,armhf,i386 |
bullseye | 2.4.0-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package exonerate: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | searching |
works-with-format | plaintext |
|
License: DFSG free
|
Exonerate allows you to align sequences using a many alignment models, using
either exhaustive dynamic programming, or a variety of heuristics. Much of
the functionality of the Wise dynamic programming suite was reimplemented in C
for better efficiency. Exonerate is an intrinsic component of the building of
the Ensembl genome databases, providing similarity scores between RNA and DNA
sequences and thus determining splice variants and coding sequences in
general.
An In-silico PCR Experiment Simulation System (see the ipcress man page) is
packaged with exonerate.
This package also comes with a selection of utilities for performing
simple manipulations quickly on fasta files beyond 2Gb
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fasta3
tools for searching collections of biological sequences
|
Versions of package fasta3 |
Release | Version | Architectures |
bullseye | 36.3.8h.2020-02-11-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 36.3.8i.14-Nov-2020-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 36.3.8i.14-Nov-2020-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 36.3.8g-1 (non-free) | amd64 |
trixie | 36.3.8i.14-Nov-2020-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
The FASTA programs find regions of local or global similarity between
Protein or DNA sequences, either by searching Protein or DNA databases,
or by identifying local duplications within a sequence. Other
programs provide information on the statistical significance of an
alignment. Like BLAST, FASTA can be used to infer functional and
evolutionary relationships between sequences as well as help identify
members of gene families.
- Protein
- Protein-protein FASTA
- Protein-protein Smith-Waterman (ssearch)
- Global Protein-protein (Needleman-Wunsch) (ggsearch)
- Global/Local protein-protein (glsearch)
- Protein-protein with unordered peptides (fasts)
-
Protein-protein with mixed peptide sequences (fastf)
-
Nucleotide
- Nucleotide-Nucleotide (DNA/RNA fasta)
- Ordered Nucleotides vs Nucleotide (fastm)
-
Un-ordered Nucleotides vs Nucleotide (fasts)
-
Translated
- Translated DNA (with frameshifts, e.g. ESTs)
vs Proteins (fastx/fasty)
- Protein vs Translated DNA (with frameshifts)
(tfastx/tfasty)
-
Peptides vs Translated DNA (tfasts)
-
Statistical Significance
- Protein vs Protein shuffle (prss)
- DNA vs DNA shuffle (prss)
-
Translated DNA vs Protein shuffle (prfx)
-
Local Duplications
- Local Protein alignments (lalign)
- Plot Protein alignment "dot-plot" (plalign)
- Local DNA alignments (lalign)
- Plot DNA alignment "dot-plot" (plalign)
This software is often used via a web service at the
EBI with readily indexed reference databases at
http://www.ebi.ac.uk/Tools/fasta/.
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fastahack
utility for indexing and sequence extraction from FASTA files
|
Versions of package fastahack |
Release | Version | Architectures |
stretch | 0.0+20160702-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el |
bullseye | 1.0.0+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.0.0+dfsg-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.0.0+dfsg-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.0.0+dfsg-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 0.0+git20160702.bbc645f+dfsg-6 | amd64,arm64,armhf,i386 |
|
License: DFSG free
|
fastahack is a small application for indexing and extracting sequences and
subsequences from FASTA files. The included Fasta.cpp library provides a FASTA
reader and indexer that can be embedded into applications which would benefit
from directly reading subsequences from FASTA files. The library automatically
handles index file generation and use.
Features:
- FASTA index (.fai) generation for FASTA files
- Sequence extraction
- Subsequence extraction
- Sequence statistics (currently only entropy is provided)
Sequence and subsequence extraction use fseek64 to provide fastest-possible
extraction without RAM-intensive file loading operations. This makes fastahack
a useful tool for bioinformaticists who need to quickly extract many
subsequences from a reference FASTA sequence.
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fastani
Fast alignment-free computation of whole-genome Average Nucleotide Identity
|
Versions of package fastani |
Release | Version | Architectures |
sid | 1.33-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.33-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.33-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
ANI is defined as mean nucleotide identity of orthologous gene pairs
shared between two microbial genomes. FastANI supports pairwise comparison
of both complete and draft genome assemblies.
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fastaq
FASTA and FASTQ file manipulation tools
|
Versions of package fastaq |
Release | Version | Architectures |
stretch | 3.14.0-1 | all |
buster | 3.17.0-2 | all |
sid | 3.17.0-9 | all |
bullseye | 3.17.0-3 | all |
bookworm | 3.17.0-5 | all |
trixie | 3.17.0-9 | all |
jessie | 1.5.0-1 | all |
|
License: DFSG free
|
Fastaq represents a diverse collection of scripts that perform useful and
common FASTA/FASTQ manipulation tasks, such as filtering, merging, splitting,
sorting, trimming, search/replace, etc. Input and output files can be gzipped
(format is automatically detected) and individual Fastaq commands can be piped
together.
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fastdnaml
Tool for construction of phylogenetic trees of DNA sequences
|
Versions of package fastdnaml |
Release | Version | Architectures |
bullseye | 1.2.2-15 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.2.2-11 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.2.2-10 | amd64,armel,armhf,i386 |
bookworm | 1.2.2-15 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.2.2-17 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.2.2-17 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.2.2-14 | amd64,arm64,armhf,i386 |
Debtags of package fastdnaml: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing, comparing |
works-with-format | plaintext |
|
License: DFSG free
|
fastDNAml is a program derived from Joseph Felsenstein's version 3.3 DNAML
(part of his PHYLIP package). Users should consult the documentation for
DNAML before using this program.
fastDNAml is an attempt to solve the same problem as DNAML, but to do so
faster and using less memory, so that larger trees and/or more bootstrap
replicates become tractable. Much of fastDNAml is merely a recoding of the
PHYLIP 3.3 DNAML program from PASCAL to C.
Note that the homepage of this program is not available any more and so
this program will probably not see any further updates.
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fastlink
faster version of pedigree programs of Linkage
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Versions of package fastlink |
Release | Version | Architectures |
bullseye | 4.1P-fix100+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 4.1P-fix100+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 4.1P-fix100+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 4.1P-fix100+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 4.1P-fix95-3 | amd64,armel,armhf,i386 |
stretch | 4.1P-fix100+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 4.1P-fix100+dfsg-2 | amd64,arm64,armhf,i386 |
Debtags of package fastlink: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing, comparing |
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License: DFSG free
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Genetic linkage analysis is a statistical technique used to map
genes and find the approximate location of disease genes. There
was a standard software package for genetic linkage called
LINKAGE. FASTLINK is a significantly modified and improved
version of the main programs of LINKAGE that runs much faster
sequentially, can run in parallel, allows the user to recover
gracefully from a computer crash, and provides abundant new
documentation. FASTLINK has been used in over 1000 published
genetic linkage studies.
This package contains the following programs:
ilink: GEMINI optimization procedure to find a locally
optimal value of the theta vector of recombination
fractions
linkmap: calculates location scores of one locus against a
fixed map of other loci
lodscore: compares likelihoods at locally optimal theta
mlink: calculates lod scores and risk with two of more loci
unknown: identify possible genotypes for unknowns
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fastml
maximum likelihood ancestral amino-acid sequence reconstruction
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Versions of package fastml |
Release | Version | Architectures |
stretch | 3.1-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 3.1-4 | amd64,arm64,armhf,i386 |
bookworm | 3.11-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 3.11-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 3.11-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 3.11-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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FastML is a bioinformatics tool for the reconstruction of ancestral
sequences based on the phylogenetic relations between homologous
sequences. FastML runs several algorithms that reconstruct the ancestral
sequences with emphasis on an accurate reconstruction of both indels and
characters. For character reconstruction the previously described FastML
algorithms are used to efficiently infer the most likely ancestral
sequences for each internal node of the tree. Both joint and the
marginal reconstructions are provided. For indels reconstruction the
sequences are first coded according to the indel events detected within
the multiple sequence alignment (MSA) and then a state-of-the-art
likelihood model is used to reconstruct ancestral indels states. The
results are the most probable sequences, together with posterior
probabilities for each character and indel at each sequence position for
each internal node of the tree. FastML is generic and is applicable for
any type of molecular sequences (nucleotide, protein, or codon
sequences).
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fastp
Ultra-fast all-in-one FASTQ preprocessor
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Versions of package fastp |
Release | Version | Architectures |
trixie | 0.23.4+dfsg-1 | amd64,arm64,armel,armhf,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.20.1+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.19.6+dfsg-1 | amd64,arm64,armhf,i386 |
sid | 0.23.4+dfsg-1 | amd64,arm64,armel,armhf,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.23.2+dfsg-2 | amd64,arm64,armel,armhf,mips64el,mipsel,ppc64el,s390x |
upstream | 0.24.0 |
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License: DFSG free
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All-in-one FASTQ preprocessor, fastp provides functions including quality
profiling, adapter trimming, read filtering and base correction. It supports
both single-end and paired-end short read data and also provides basic support
for long-read data.
The package is enhanced by the following packages:
multiqc
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fastq-pair
Rewrites paired end fastq so all reads have a mate to separate out singletons
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Versions of package fastq-pair |
Release | Version | Architectures |
sid | 1.0-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.0-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.0-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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This package rewrites the fastq files with the sequences in order,
with matching files for the two files provided on the command line,
and then any single reads that are not matched are place in two separate
files, one for each original file.
This code is designed to be fast and memory efficient, and works with large
fastq files. It does not store the whole file in memory, but rather just stores
the locations of each of the indices in the first file provided in memory.
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fastqc
quality control for high throughput sequence data
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Versions of package fastqc |
Release | Version | Architectures |
trixie | 0.12.1+dfsg-4 | all |
bookworm | 0.11.9+dfsg-6 | all |
bullseye | 0.11.9+dfsg-4 | all |
jessie | 0.11.2+dfsg-3 | all |
buster | 0.11.8+dfsg-2 | all |
stretch | 0.11.5+dfsg-6 | all |
sid | 0.12.1+dfsg-4 | all |
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License: DFSG free
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FastQC aims to provide a simple way to do some quality control checks on
raw sequence data coming from high throughput sequencing pipelines. It
provides a modular set of analyses which you can use to give a quick
impression of whether your data has any problems of which you should
be aware before doing any further analysis.
The main functions of FastQC are
- Import of data from BAM, SAM or FastQ files (any variant)
- Providing a quick overview to tell you in which areas there may
be problems
- Summary graphs and tables to quickly assess your data
- Export of results to an HTML based permanent report
- Offline operation to allow automated generation of reports without
running the interactive application
The package is enhanced by the following packages:
multiqc
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fastqtl
Quantitative Trait Loci (QTL) mapper in cis for molecular phenotypes
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Versions of package fastqtl |
Release | Version | Architectures |
bookworm | 2.184+v7+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 2.184+dfsg-5 | amd64,arm64,armel,i386,mips64el,mipsel,ppc64el |
buster | 2.184+dfsg-6 | amd64,arm64,armhf |
bullseye | 2.184+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.184+v7+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.184+v7+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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The goal of FastQTL is to identify single-nucleotide polymorphisms (SNPs)
which are significantly associated with various molecular phenotypes
(i.e. expression of known genes, cytosine methylation levels, etc).
It performs scans for all possible phenotype-variant pairs in cis
(i.e. variants located within a specific window around a phenotype).
FastQTL implements a new permutation scheme (Beta approximation) to accurately
and rapidly correct for multiple-testing at both the genotype and phenotype
levels.
The package is enhanced by the following packages:
fastqtl-doc
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fasttree
phylogenetic trees from alignments of nucleotide or protein sequences
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Versions of package fasttree |
Release | Version | Architectures |
bullseye | 2.1.11-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.1.10-2 | amd64,arm64,armhf,i386 |
jessie | 2.1.7-2 | amd64,armel,armhf,i386 |
stretch | 2.1.9-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2.1.11-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 2.1.11-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.1.11-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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FastTree infers approximately-maximum-likelihood phylogenetic trees from
alignments of nucleotide or protein sequences. It handles alignments
with up to a million of sequences in a reasonable amount of time and
memory. For large alignments, FastTree is 100-1,000 times faster than
PhyML 3.0 or RAxML 7.
FastTree is more accurate than PhyML 3 with default settings, and much
more accurate than the distance-matrix methods that are traditionally
used for large alignments. FastTree uses the Jukes-Cantor or generalized
time-reversible (GTR) models of nucleotide evolution and the JTT
(Jones-Taylor-Thornton 1992) model of amino acid evolution. To account
for the varying rates of evolution across sites, FastTree uses a single
rate for each site (the "CAT" approximation). To quickly estimate the
reliability of each split in the tree, FastTree computes local support
values with the Shimodaira-Hasegawa test (these are the same as PhyML 3's
"SH-like local supports").
This package contains a single threaded version (fasttree) and a
parallel version which uses OpenMP (fasttreMP).
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ffindex
simple index/database for huge amounts of small files
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Versions of package ffindex |
Release | Version | Architectures |
buster | 0.9.9.9-2 | amd64,arm64,armhf,i386 |
trixie | 0.9.9.9-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 0.9.9.7-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.9.9.9-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 0.9.9.3-2 | amd64,armel,armhf,i386 |
sid | 0.9.9.9-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.9.9.9-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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FFindex is a very simple index/database for huge amounts of small files. The
files are stored concatenated in one big data file, separated by '\0'. A
second file contains a plain text index, giving name, offset and length of
the small files. The lookup is currently done with a binary search on an
array made from the index file.
This package provides the executables.
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figtree
graphical phylogenetic tree viewer
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Versions of package figtree |
Release | Version | Architectures |
sid | 1.4.4-6 | all |
stretch | 1.4.2+dfsg-2 | all |
buster | 1.4.4-3 | all |
jessie | 1.4-2 | all |
bookworm | 1.4.4-5 | all |
trixie | 1.4.4-6 | all |
bullseye | 1.4.4-5 | all |
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License: DFSG free
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FigTree is designed as a graphical viewer of phylogenetic trees and as
a program for producing publication-ready figures. In particular it is
designed to display summarized and annotated trees produced by BEAST.
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filtlong
quality filtering tool for long reads of genome sequences
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Versions of package filtlong |
Release | Version | Architectures |
trixie | 0.2.1-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.2.1-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.2.1-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.2.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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Filtlong is a tool for filtering long reads by quality. It can take a
set of long reads and produce a smaller, better subset. It uses both
read length (longer is better) and read identity (higher is better) when
choosing which reads pass the filter.
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fitgcp
fitting genome coverage distributions with mixture models
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Versions of package fitgcp |
Release | Version | Architectures |
bookworm | 0.0.20150429-5 | all |
trixie | 0.0.20150429-5 | all |
sid | 0.0.20150429-5 | all |
bullseye | 0.0.20150429-4 | all |
buster | 0.0.20150429-2 | amd64,arm64 |
stretch | 0.0.20150429-1 | amd64,arm64,mips64el,ppc64el |
jessie | 0.0.20130418-2 | amd64,i386 |
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License: DFSG free
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Genome coverage, the number of sequencing reads mapped to a position in
a genome, is an insightful indicator of irregularities within sequencing
experiments. While the average genome coverage is frequently used within
algorithms in computational genomics, the complete information available
in coverage profiles (i.e. histograms over all coverages) is currently
not exploited to its full extent. Thus, biases such as fragmented or
erroneous reference genomes often remain unaccounted for. Making this
information accessible can improve the quality of sequencing experiments
and quantitative analyses.
fitGCP is a framework for fitting mixtures of probability distributions
to genome coverage profiles. Besides commonly used distributions, fitGCP
uses distributions tailored to account for common artifacts. The mixture
models are iteratively fitted based on the Expectation-Maximization
algorithm.
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flash
Fast Length Adjustment of SHort reads
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Versions of package flash |
Release | Version | Architectures |
trixie | 1.2.11-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.2.11-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.2.11-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.2.11-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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FLASH (Fast Length Adjustment of SHort reads) is a very fast and
accurate software tool to merge paired-end reads from next-generation
sequencing experiments. FLASH is designed to merge pairs of reads when
the original DNA fragments are shorter than twice the length of reads.
The resulting longer reads can significantly improve genome assemblies.
They can also improve transcriptome assembly when FLASH is used to merge
RNA-seq data.
The package is enhanced by the following packages:
multiqc
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flexbar
flexible barcode and adapter removal for sequencing platforms
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Versions of package flexbar |
Release | Version | Architectures |
experimental | 3.5.0-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 3.5.0-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 3.4.0-2 | amd64,arm64,armhf,i386 |
jessie | 2.50-1 | amd64,armhf,i386 |
trixie | 3.5.0-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 3.5.0-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 2.50-2 | amd64,arm64,armhf,i386,mips,mips64el,mipsel,ppc64el |
sid | 3.5.0-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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Flexbar preprocesses high-throughput sequencing data efficiently. It
demultiplexes barcoded runs and removes adapter sequences. Moreover,
trimming and filtering features are provided. Flexbar increases mapping
rates and improves genome and transcriptome assemblies. It supports
next-generation sequencing data in fasta/q and csfasta/q format from
Illumina, Roche 454, and the SOLiD platform.
Parameter names changed in Flexbar. Please review scripts. The recent
months, default settings were optimised, several bugs were fixed and
various improvements were made, e.g. revamped command-line interface,
new trimming modes as well as lower time and memory requirements.
The package is enhanced by the following packages:
multiqc
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flye
de novo assembler for single molecule sequencing reads using repeat graphs
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Versions of package flye |
Release | Version | Architectures |
sid | 2.9.5+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.9.1+dfsg-1 | amd64,arm64,mips64el,ppc64el,s390x |
trixie | 2.9.5+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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Flye is a de novo assembler for single molecule sequencing reads, such
as those produced by PacBio and Oxford Nanopore Technologies. It is
designed for a wide range of datasets, from small bacterial projects to
large mammalian-scale assemblies. The package represents a complete
pipeline: it takes raw PacBio / ONT reads as input and outputs polished
contigs. Flye also has a special mode for metagenome assembly.
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fml-asm
tool for assembling Illumina short reads in small regions
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Versions of package fml-asm |
Release | Version | Architectures |
buster | 0.1-5 | amd64 |
trixie | 0.1+git20221215.85f159e-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.1+git20190320.b499514-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.1+git20221215.85f159e-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.1+git20190320.b499514-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 0.1-2 | amd64 |
stretch-backports | 0.1-4~bpo9+1 | amd64 |
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License: DFSG free
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Fml-asm is a command-line tool for assembling Illumina short reads in regions
from 100bp to 10 million bp in size, based on the fermi-lite library.
It is largely a light-weight in-memory version of fermikit without
generating any intermediate files. It inherits the performance, the relatively
small memory footprint and the features of fermikit. In particular, fermi-lite
is able to retain heterozygous events and thus can be used to assemble diploid
regions for the purpose of variant calling.
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freebayes
Bayesian haplotype-based polymorphism discovery and genotyping
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Versions of package freebayes |
Release | Version | Architectures |
experimental | 1.3.7-1~exp | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x |
buster | 1.2.0-2 | amd64 |
stretch-backports | 1.2.0-1~bpo9+1 | amd64 |
bullseye | 1.3.5-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.3.6-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.3.7-1 | amd64,arm64,mips64el,ppc64el,riscv64 |
upstream | 1.3.8-pre3 |
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License: DFSG free
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FreeBayes is a Bayesian genetic variant detector designed to find
small polymorphisms, specifically SNPs (single-nucleotide
polymorphisms), indels (insertions and deletions), MNPs
(multi-nucleotide polymorphisms), and complex events (composite
insertion and substitution events) smaller than the length of a
short-read sequencing alignment.
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freecontact
fast protein contact predictor
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Versions of package freecontact |
Release | Version | Architectures |
trixie | 1.0.21-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.0.21-13 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.21-7 | amd64,arm64,armhf,i386 |
jessie | 1.0.21-3 | amd64,armel,armhf,i386 |
bullseye | 1.0.21-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.0.21-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.0.21-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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FreeContact is a protein residue contact predictor optimized for speed.
Its input is a multiple sequence alignment. FreeContact can function as an
accelerated drop-in for the published contact predictors
EVfold-mfDCA of DS. Marks (2011) and
PSICOV of D. Jones (2011).
FreeContact is accelerated by a combination of vector instructions, multiple
threads, and faster implementation of key parts.
Depending on the alignment, 8-fold or higher speedups are possible.
A sufficiently large alignment is required for meaningful results.
As a minimum, an alignment with an effective (after-weighting) sequence count
bigger than the length of the query sequence should be used. Alignments with
tens of thousands of (effective) sequences are considered good input.
jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite
can be used to generate the alignments, for example.
This package contains the command line tool freecontact(1).
Topics: Structure prediction; Sequence analysis
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fsa
Fast Statistical Alignment of protein, RNA or DNA sequences
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Versions of package fsa |
Release | Version | Architectures |
bullseye | 1.15.9+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.15.9+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.15.9+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.15.9+dfsg-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.15.9+dfsg-4 | amd64,arm64,armhf,i386 |
bookworm | 1.15.9+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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FSA is a probabilistic multiple sequence alignment algorithm which uses
a "distance-based" approach to aligning homologous protein, RNA or DNA
sequences. Much as distance-based phylogenetic reconstruction methods
like Neighbor-Joining build a phylogeny using only pairwise divergence
estimates, FSA builds a multiple alignment using only pairwise
estimations of homology. This is made possible by the sequence annealing
technique for constructing a multiple alignment from pairwise
comparisons, developed by Ariel Schwartz.
FSA brings the high accuracies previously available only for
small-scale analyses of proteins or RNAs to large-scale problems such as
aligning thousands of sequences or megabase-long sequences. FSA
introduces several novel methods for constructing better alignments:
- FSA uses machine-learning techniques to estimate gap and
substitution parameters on the fly for each set of input sequences.
This "query-specific learning" alignment method makes FSA very robust:
it can produce superior alignments of sets of homologous sequences
which are subject to very different evolutionary constraints.
- FSA is capable of aligning hundreds or even thousands of sequences
using a randomized inference algorithm to reduce the computational
cost of multiple alignment. This randomized inference can be over ten
times faster than a direct approach with little loss of accuracy.
- FSA can quickly align very long sequences using the "anchor
annealing" technique for resolving anchors and projecting them with
transitive anchoring. It then stitches together the alignment between
the anchors using the methods described above.
- The included GUI, MAD (Multiple Alignment Display), can display the
intermediate alignments produced by FSA, where each character is
colored according to the probability that it is correctly aligned
Please cite:
Robert K. Bradley, Adam Roberts, Michael Smoot, Sudeep Juvekar, Jaeyoung Do, Colin Dewey, Ian Holmes and Lior Pachter:
Fast Statistical Alignment.
(PubMed,eprint)
PLoS Comput Biol.
5(5):e1000392
(2009)
|
|
fsm-lite
frequency-based string mining (lite)
|
Versions of package fsm-lite |
Release | Version | Architectures |
trixie | 1.0-8 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
stretch | 1.0-2 | amd64,arm64,mips64el,ppc64el,s390x |
buster | 1.0-3 | amd64,arm64 |
bullseye | 1.0-5 | amd64,arm64,mips64el,ppc64el,s390x |
bookworm | 1.0-8 | amd64,arm64,mips64el,ppc64el,s390x |
sid | 1.0-8 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
A singe-core implementation of frequency-based substring mining used in
bioinformatics to extract substrings that discriminate two (or more)
datasets inside high-throughput sequencing data.
|
|
gamgi
General Atomistic Modelling Graphic Interface (GAMGI)
|
Versions of package gamgi |
Release | Version | Architectures |
bookworm | 0.17.5-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.17.3-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.17.3-2 | amd64,arm64,armhf,i386 |
jessie | 0.17.1-1 | amd64,armel,armhf,i386 |
stretch | 0.17.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 0.17.5-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package gamgi: |
role | program |
uitoolkit | gtk |
|
License: DFSG free
|
The General Atomistic Modelling Graphic Interface (GAMGI) provides
a graphical interface to build, view and analyze atomic structures.
The program is aimed at the scientific community and provides a
graphical interface to study atomic structures and to prepare images
for presentations, and for teaching the atomic structure of matter.
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|
garli
phylogenetic analysis of molecular sequence data using maximum-likelihood
|
Versions of package garli |
Release | Version | Architectures |
sid | 2.1-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 2.1-3 | amd64,arm64,armhf,i386 |
bullseye | 2.1-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.1-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 2.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
GARLI, Genetic Algorithm for Rapid Likelihood Inference is a program for
inferring phylogenetic trees. Using an approach similar to a classical
genetic algorithm, it rapidly searches the space of evolutionary trees
and model parameters to find the solution maximizing the likelihood
score. It implements nucleotide, amino acid and codon-based models of
sequence evolution, and runs on all platforms. The latest version adds
support for partitioned models and morphology-like datatypes.
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|
garlic
visualization program for biomolecules
|
Versions of package garlic |
Release | Version | Architectures |
trixie | 1.6-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.6-1.1 | amd64,armel,armhf,i386 |
bookworm | 1.6-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.6-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.6-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.6-3 | amd64,arm64,armhf,i386 |
stretch | 1.6-1.1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package garlic: |
field | biology, chemistry |
interface | x11 |
role | program |
scope | utility |
uitoolkit | xlib |
use | viewing |
x11 | application |
|
License: DFSG free
|
Garlic is written for the investigation of membrane proteins. It may be
used to visualize other proteins, as well as some geometric objects.
This version of garlic recognizes PDB format version 2.1. Garlic may
also be used to analyze protein sequences.
It only depends on the X libraries, no other libraries are needed.
Features include:
- The slab position and thickness are visible in a small window.
- Atomic bonds as well as atoms are treated as independent drawable
objects.
- The atomic and bond colors depend on position. Five mapping modes
are available (as for slab).
- Capable to display stereo image.
- Capable to display other geometric objects, like membrane.
- Atomic information is available for atom covered by the mouse
pointer. No click required, just move the mouse pointer over the
structure!
- Capable to load more than one structure.
- Capable to draw Ramachandran plot, helical wheel, Venn diagram,
averaged hydrophobicity and hydrophobic moment plot.
- The command prompt is available at the bottom of the main window.
It is able to display one error message and one command string.
Please cite:
Damir Zucic and Davor Juretic:
Precise Annotation of Transmembrane Segments with Garlic - a Free Molecular Visualization Program
(eprint)
Croatica Chemica Acta
77(1-2):397-401
(2004)
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|
gasic
genome abundance similarity correction
|
Versions of package gasic |
Release | Version | Architectures |
sid | 0.0.r19-8 | all |
bookworm | 0.0.r19-8 | all |
jessie | 0.0.r18-2 | amd64 |
stretch | 0.0.r19-1 | amd64 |
buster | 0.0.r19-4 | amd64 |
bullseye | 0.0.r19-7 | all |
trixie | 0.0.r19-8 | all |
|
License: DFSG free
|
One goal of sequencing based metagenomic analysis is the quantitative
taxonomic assessment of microbial community compositions. However, the
majority of approaches either quantify at low resolution (e.g. at phylum
level) or have severe problems discerning highly similar species. Yet,
accurate quantification on species level is desirable in applications
such as metagenomic diagnostics or community comparison. GASiC is a
method to correct read alignment results for the ambiguities imposed by
similarities of genomes. It has superior performance over existing
methods.
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gatb-core
Genome Analysis Toolbox with de-Bruijn graph
|
Versions of package gatb-core |
Release | Version | Architectures |
buster | 1.4.1+git20181225.44d5a44+dfsg-3 | amd64,arm64,i386 |
bookworm | 1.4.2+dfsg-11 | amd64,arm64,mips64el,ppc64el |
bullseye | 1.4.2+dfsg-6 | amd64,arm64,i386,mips64el,ppc64el,s390x |
sid | 1.4.2+dfsg-13 | amd64,arm64,mips64el,ppc64el,riscv64 |
trixie | 1.4.2+dfsg-13 | amd64,arm64,mips64el,ppc64el,riscv64 |
|
License: DFSG free
|
The GATB-CORE project provides a set of highly efficient
algorithms to analyse NGS data sets. These methods enable
the analysis of data sets of any size on multi-core desktop
computers, including very huge amount of reads data coming
from any kind of organisms such as bacteria, plants,
animals and even complex samples (e.g. metagenomes).
Read more about GATB at https://gatb.inria.fr/.
By itself GATB-CORE is not an NGS data analysis tool.
However, it can be used to create such tools. There already
exist a set of ready-to-use tools relying on GATB-CORE
library: see https://gatb.inria.fr/software/
Please cite:
Erwan Drezen, Guillaume Rizk, Rayan Chikhi, Charles Deltel, Claire Lemaitre, Pierre Peterlongo and Dominique Lavenier:
GATB: Genome Assembly & Analysis Tool Box.
Bioinformatics
30(20):2959-2961
(2014)
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gbrowse
GMOD Generic Genome Browser
|
Versions of package gbrowse |
Release | Version | Architectures |
trixie | 2.56+dfsg-12 | all |
sid | 2.56+dfsg-12 | all |
bookworm | 2.56+dfsg-11 | all |
bullseye | 2.56+dfsg-8 | all |
buster | 2.56+dfsg-4 | all |
stretch | 2.56+dfsg-2 | all |
jessie | 2.54+dfsg-3 | all |
Debtags of package gbrowse: |
field | biology, biology:bioinformatics |
interface | web |
role | program |
use | analysing, viewing |
web | application, cgi |
|
License: DFSG free
|
Generic Genome Browser is a simple but highly
configurable web-based genome browser. It is a component of the
Generic Model Organism Systems Database project (GMOD).
Some of its features:
- Simultaneous bird's eye and detailed views of the genome;
- Scroll, zoom, center;
- Attach arbitrary URLs to any annotation;
- Order and appearance of tracks are customizable by administrator and
end-user;
- Search by annotation ID, name, or comment;
- Supports third party annotation using GFF formats;
- Settings persist across sessions;
- DNA and GFF dumps;
- Connectivity to different databases, including BioSQL and Chado;
- Multi-language support;
- Third-party feature loading;
- Customizable plug-in architecture (e.g. run BLAST, dump & import many
formats, find oligonucleotides, design primers, create restriction maps,
edit features).
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gdpc
visualiser of molecular dynamic simulations
|
Versions of package gdpc |
Release | Version | Architectures |
jessie | 2.2.5-3 | amd64,armel,armhf,i386 |
stretch | 2.2.5-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.2.5-14 | amd64,arm64,mips64el,ppc64el |
bookworm | 2.2.5-15 | amd64,arm64,mips64el,ppc64el |
buster | 2.2.5-9 | amd64,arm64,armhf,i386 |
trixie | 2.2.5-16 | amd64,arm64,mips64el,ppc64el,riscv64 |
sid | 2.2.5-16 | amd64,arm64,mips64el,ppc64el,riscv64 |
Debtags of package gdpc: |
field | biology, biology:structural, chemistry, physics |
interface | x11 |
role | program |
scope | application |
uitoolkit | gtk |
use | viewing |
works-with | 3dmodel, image, video |
works-with-format | jpg, png |
x11 | application |
|
License: DFSG free
|
gpdc is a graphical program for visualising output data from
molecular dynamics simulations. It reads input in the standard xyz
format, as well as other custom formats, and can output pictures of
each frame in JPG or PNG format.
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gemma
Genome-wide Efficient Mixed Model Association
|
Versions of package gemma |
Release | Version | Architectures |
trixie | 0.98.5+dfsg-3 | amd64,arm64,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.98.5+dfsg-3 | amd64,arm64,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 0.98.1+dfsg-1 | amd64,arm64,armhf,i386 |
bullseye | 0.98.4+dfsg-4 | amd64,arm64,armhf,i386,mips64el,ppc64el,s390x |
bookworm | 0.98.5+dfsg-2 | amd64,arm64,armhf,i386,mips64el,ppc64el,s390x |
|
License: DFSG free
|
GEMMA is the software implementing the Genome-wide Efficient Mixed
Model Association algorithm for a standard linear mixed model and some
of its close relatives for genome-wide association studies (GWAS):
- It fits a univariate linear mixed model (LMM) for marker association
tests with a single phenotype to account for population stratification
and sample structure, and for estimating the proportion of variance in
phenotypes explained (PVE) by typed genotypes (i.e. "chip heritability").
- It fits a multivariate linear mixed model (mvLMM) for testing marker
associations with multiple phenotypes simultaneously while controlling
for population stratification, and for estimating genetic correlations
among complex phenotypes.
- It fits a Bayesian sparse linear mixed model (BSLMM) using Markov
chain Monte Carlo (MCMC) for estimating PVE by typed genotypes,
predicting phenotypes, and identifying associated markers by jointly
modeling all markers while controlling for population structure.
- It estimates variance component/chip heritability, and partitions
it by different SNP functional categories. In particular, it uses HE
regression or REML AI algorithm to estimate variance components when
individual-level data are available. It uses MQS to estimate variance
components when only summary statisics are available.
GEMMA is computationally efficient for large scale GWAS and uses freely
available open-source numerical libraries.
Please cite:
Xiang Zhou and Matthew Stephens:
Genome-wide efficient mixed-model analysis for association studies
Nature Genetics
44:821-824
(2012)
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genometester
toolkit for performing set operations on k-mer lists
|
Versions of package genometester |
Release | Version | Architectures |
bookworm | 4.0+git20200511.91cecb5+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 4.0+git20180508.a9c14a6+dfsg-1 | amd64,arm64,armhf,i386 |
trixie | 4.0+git20200511.91cecb5+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 4.0+git20200511.91cecb5+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 4.0+git20200511.91cecb5+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 4.0+git20221122.71e6625 |
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License: DFSG free
|
Toolkit for performing set operations - union, intersection and
complement - on k-mer lists.
GenomeTester4 toolkit, which contains a novel tool GListCompare for
performing union, intersection and complement (difference) set
operations on k-mer lists. It contains examples of how these
general operations can be combined to solve a variety of biological
analysis tasks.
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genomethreader
software tool to compute gene structure predictions
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Versions of package genomethreader |
Release | Version | Architectures |
trixie | 1.7.3+dfsg-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.7.3+dfsg-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.7.3+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.7.3+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
GenomeThreader is a software tool to compute gene structure predictions.
The gene structure predictions are calculated using a similarity-based
approach where additional cDNA/EST and/or protein sequences are used to
predict gene structures via spliced alignments. GenomeThreader was motivated
by disabling limitations in GeneSeqer, a popular gene prediction program
which is widely used for plant genome annotation.
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genometools
versatile genome analysis toolkit
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Versions of package genometools |
Release | Version | Architectures |
bullseye-backports-sloppy | 1.6.5+ds-2~bpo11+1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.6.2+ds-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.6.1+ds-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster-backports | 1.6.1+ds-3~bpo10+1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 1.5.9+ds-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.5.10+ds-3 | amd64,arm64,armhf,i386 |
sid | 1.6.5+ds-2.2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.6.5+ds-2.2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm-backports | 1.6.5+ds-2~bpo12+1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.5.3-2 | amd64,armel,armhf,i386 |
Debtags of package genometools: |
biology | nuceleic-acids |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
uitoolkit | ncurses |
|
License: DFSG free
|
The GenomeTools contains a collection of useful tools for biological
sequence analysis and -presentation combined into a single binary.
The toolkit contains binaries for sequence and annotation handling, sequence
compression, index structure generation and access, annotation visualization,
and much more.
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genomicsdb-tools
sparse array storage library for genomics (tools)
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Versions of package genomicsdb-tools |
Release | Version | Architectures |
sid | 1.5.4-2 | amd64,mips64el |
bookworm | 1.4.4-3 | amd64,mips64el |
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License: DFSG free
|
GenomicsDB is built on top of a htslib fork and an internal array storage
system for importing, querying and transforming variant data. Variant data is
sparse by nature (sparse relative to the whole genome) and using sparse array
data stores is a perfect fit for storing such data.
The GenomicsDB stores variant data in a 2D array where:
- Each column corresponds to a genomic position (chromosome + position);
- Each row corresponds to a sample in a VCF (or CallSet in the GA4GH
terminology);
- Each cell contains data for a given sample/CallSet at a given position;
data is stored in the form of cell attributes;
- Cells are stored in column major order - this makes accessing cells with
the same column index (i.e. data for a given genomic position over all
samples) fast.
- Variant interval/gVCF interval data is stored in a cell at the start of the
interval. The END is stored as a cell attribute. For variant intervals
(such as deletions and gVCF REF blocks), an additional cell is stored at
the END value of the variant interval. When queried for a given genomic
position, the query library performs an efficient sweep to determine all
intervals that intersect with the queried position.
This package contains some tools to be run as executable files.
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gentle
??? missing short description for package gentle :-(
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Versions of package gentle |
Release | Version | Architectures |
bullseye | 1.9+cvs20100605+dfsg1-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.9+cvs20100605+dfsg1-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.9.5~alpha2+dfsg1-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.9+cvs20100605+dfsg1-3 | amd64,armel,armhf,i386 |
sid | 1.9.5~alpha2+dfsg1-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.9+cvs20100605+dfsg1-7 | amd64,arm64,armhf,i386 |
stretch | 1.9+cvs20100605+dfsg1-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package gentle: |
biology | nuceleic-acids, peptidic |
field | biology, biology:bioinformatics |
interface | x11 |
role | program |
uitoolkit | wxwidgets |
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License: DFSG free
|
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gff2aplot
pair-wise alignment-plots for genomic sequences in PostScript
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Versions of package gff2aplot |
Release | Version | Architectures |
trixie | 2.0-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 2.0-7 | amd64,armel,armhf,i386 |
stretch | 2.0-8 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.0-11 | amd64,arm64,armhf,i386 |
bullseye | 2.0-13 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.0-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.0-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package gff2aplot: |
field | biology, biology:bioinformatics |
interface | commandline, shell |
role | program |
scope | utility |
use | converting, viewing |
works-with | image:vector |
works-with-format | plaintext, postscript |
|
License: DFSG free
|
A program to visualize the alignment of two genomic sequences together with
their annotations. From GFF-format input files it produces PostScript figures
for that alignment.
The following menu lists many features of gff2aplot:
- Comprehensive alignment plots for any GFF-feature. Attributes are defined
separately so you can modify only whatsoever attributes for a given file or
share same customization across different data-sets.
- All parameters are set by default within the program, but it can be also
fully configured via gff2ps-like flexible customization files. Program can
handle several of such files, summarizing all the settings before producing
the corresponding figure. Moreover, all customization parameters can be set
via command-line switches, which allows users to play with those parameters
before adding any to a customization file.
- Source order is taken from input files, if you swap file order you can
visualize alignment and its annotation with the new input arrangement.
- All alignment scores can be visualized in a PiP box below gff2aplot area,
using grey-color scale, user-defined color scale or score-dependent
gradients.
- Scalable fonts, which can also be chosen among the basic PostScript default
fonts. Feature and group labels can be rotated to improve readability in
both annotation axes.
- The program is still defined as a Unix filter so it can handle data from
files, redirections and pipes, writing output to standard-output and
warnings to standard error.
- gff2aplot is able to manage many physical page formats (from A0 to A10, and
more -see available page sizes in its manual-), including user-defined ones.
This allows, for instance, the generation of poster size genomic maps, or
the use of a continuous-paper supporting plotting device, either in portrait
or landscape.
- You can draw different alignments on same alignment plot and distinguish
them by using different colors for each.
- Shape dictionary has been expanded, so that further feature shapes are now
available (see manual).
- Annotation projections through alignment plots (so called ribbons) emulate
transparencies via complementary color fill patterns. This feature allows
one to show color pseudo-blending when horizontal and vertical ribbons
overlap.
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gff2ps
produces PostScript graphical output from GFF-files
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Versions of package gff2ps |
Release | Version | Architectures |
trixie | 0.98l-6 | all |
sid | 0.98l-6 | all |
jessie | 0.98d-4 | all |
stretch | 0.98d-5 | all |
buster | 0.98l-2 | all |
bullseye | 0.98l-4 | all |
bookworm | 0.98l-6 | all |
Debtags of package gff2ps: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | converting, viewing |
works-with | image:vector |
works-with-format | postscript |
|
License: DFSG free
|
gff2ps is a script program developed with the aim of converting gff-formatted
records into high quality one-dimensional plots in PostScript. Such plots
maybe useful for comparing genomic structures and to visualizing outputs from
genome annotation programs.
It can be used in a very simple way, because it assumes that the GFF file
itself carries enough formatting information, but it also allows through a
number of options and/or a configuration file, for a great degree of
customization.
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gffread
GFF/GTF format conversions, region filtering, FASTA sequence extraction
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Versions of package gffread |
Release | Version | Architectures |
bullseye | 0.12.1-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.12.7-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.12.7-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.12.7-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
Gffread is a GFF/GTF parsing utility providing format conversions,
region filtering, FASTA sequence extraction and more.
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ggd-utils
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Versions of package ggd-utils |
Release | Version | Architectures |
trixie | 1.0.0+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.0.7+ds-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.0.0+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.0.0+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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Takes a genome file and (currently) a .vcf.gz or
a .bed.gz and checks that:
* a .tbi is present
* the VCF has ""##fileformat=VCF" as the first
line
* the VCF has a #CHROM header
* the chromosome are in the order specified by
the genome file (and present)
* the positions are sorted
* the positions are <= the chromosome lengths
defined in the genome file.
As a result, any new genome going into GGD will have
a .genome file that will dictate the sort order
and presence or absence of the 'chr' prefix for chromosomes
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ghemical
GNOME molecular modelling environment
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Versions of package ghemical |
Release | Version | Architectures |
buster | 3.0.0-4 | amd64,arm64,armhf,i386 |
bookworm | 3.0.0-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 3.0.0-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x |
bullseye | 3.0.0-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 3.0.0-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package ghemical: |
field | chemistry |
interface | 3d, x11 |
role | program |
suite | gnome |
uitoolkit | gtk |
use | editing, learning, viewing |
works-with | 3dmodel |
x11 | application |
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License: DFSG free
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Ghemical is a computational chemistry software package written in C++.
It has a graphical user interface and it supports both quantum-
mechanics (semi-empirical) models and molecular mechanics models.
Geometry optimization, molecular dynamics and a large set of
visualization tools using OpenGL are currently available.
Ghemical relies on external code to provide the quantum-mechanical
calculations. Semi-empirical methods MNDO, MINDO/3, AM1 and PM3 come
from the MOPAC7 package (Public Domain), and are included in the
package. The MPQC package is used to provide ab initio methods: the
methods based on Hartree-Fock theory are currently supported with
basis sets ranging from STO-3G to 6-31G**.
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ghmm
General Hidden-Markov-Model library - tools
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Versions of package ghmm |
Release | Version | Architectures |
sid | 0.9~rc3-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.9~rc3-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.9~rc3-2 | amd64,arm64,armhf,i386 |
bullseye | 0.9~rc3-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.9~rc3-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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The General Hidden Markov Model Library (GHMM) is a C library with
additional Python3 bindings implementing a wide range of types of
Hidden Markov Models and algorithms: discrete, continuous emissions,
basic training, HMM clustering, HMM mixtures.
This package contains some tools using the library.
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glam2
gapped protein motifs from unaligned sequences
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Versions of package glam2 |
Release | Version | Architectures |
bookworm | 1064-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1064-3 | amd64,armel,armhf,i386 |
buster | 1064-5 | amd64,arm64,armhf,i386 |
stretch | 1064-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1064-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1064-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1064-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package glam2: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing, comparing, searching |
works-with-format | plaintext |
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License: DFSG free
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GLAM2 is a software package for finding motifs in sequences, typically
amino-acid or nucleotide sequences. A motif is a re-occurring sequence
pattern: typical examples are the TATA box and the CAAX prenylation motif. The
main innovation of GLAM2 is that it allows insertions and deletions in motifs.
This package includes programs for discovering motifs shared by a set of
sequences and finding matches to these motifs in a sequence database, as well
as utilities for converting glam2 motifs to standard alignment formats,
masking glam2 motifs out of sequences so that weaker motifs can be found, and
removing highly similar members of a set of sequences.
The package includes these programs:
glam2: discovering motifs shared by a set of sequences;
glam2scan: finding matches, in a sequence database, to a motif discovered
by glam2;
glam2format: converting glam2 motifs to standard alignment formats;
glam2mask: masking glam2 motifs out of sequences, so that weaker motifs
can be found;
glam2-purge: removing highly similar members of a set of sequences.
In this binary package, the fast Fourier algorithm (FFT) was enabled for the
glam2 program.
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gmap
spliced and SNP-tolerant alignment for mRNA and short reads
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Versions of package gmap |
Release | Version | Architectures |
trixie | 2024-11-20+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
sid | 2024-11-20+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
jessie | 2014-10-22-1 (non-free) | amd64 |
bookworm | 2021-12-17+ds-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
stretch | 2017-01-14-1 (non-free) | amd64 |
buster | 2019-01-24-1 (non-free) | amd64 |
bullseye | 2021-02-22+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
Debtags of package gmap: |
field | biology, biology:bioinformatics, biology:structural |
role | program |
use | analysing |
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License: DFSG free
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This package contains the programs GMAP and GSNAP as well as
utilities to manage genome databases in GMAP/GSNAP format.
GMAP (Genomic Mapping and Alignment Program) is a tool for aligning
EST, mRNA and cDNA sequences.
GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool for
aligning single-end and paired-end transcriptome reads.
Both tools can use a database of
- known splice sites and identify novel splice sites.
- known single-nucleotide polymorphisms (SNPs).
GSNAP can align bisulfite-treated DNA.
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grabix
wee tool for random access into BGZF files
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Versions of package grabix |
Release | Version | Architectures |
sid | 0.1.7-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.1.7-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.1.7-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.1.7-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
buster | 0.1.7-1 | amd64,arm64,armhf |
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License: DFSG free
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In biomedical research it is increasing practice to study
the genetic basis of disease. This now frequently comprises
the sequencing of human sequences. The output of the machine
however is redundant, and the real sequence is the best
sequence to explain the redundancy. The exchange of data
happens only with compressed files - to huge and redundant
to perform otherwise. One should avoid uncompression whenever
possible.
grabix leverages the fantastic BGZF library of the samtools
package to provide random access into text files that have
been compressed with bgzip. grabix creates it's own index
(.gbi) of the bgzipped file. Once indexed, one can extract
arbitrary lines from the file with the grab command. Or
choose random lines with the, well, random command.
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graphlan
circular representations of taxonomic and phylogenetic trees
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Versions of package graphlan |
Release | Version | Architectures |
sid | 1.1.3-6 | all |
stretch | 1.1-2 | all |
buster | 1.1.3-1 | all |
bullseye | 1.1.3-2 | all |
bookworm | 1.1.3-4 | all |
trixie | 1.1.3-6 | all |
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License: DFSG free
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GraPhlAn is a software tool for producing high-quality circular
representations of taxonomic and phylogenetic trees. It focuses on
concise, integrative, informative, and publication-ready representations
of phylogenetically- and taxonomically-driven investigation.
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grinder
Versatile omics shotgun and amplicon sequencing read simulator
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Versions of package grinder |
Release | Version | Architectures |
buster | 0.5.4-5 | all |
bullseye | 0.5.4-6 | all |
sid | 0.5.4-6 | all |
trixie | 0.5.4-6 | all |
bookworm | 0.5.4-6 | all |
jessie | 0.5.3-3 | all |
stretch | 0.5.4-1 | all |
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License: DFSG free
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Grinder is a versatile program to create random shotgun and amplicon sequence
libraries based on DNA, RNA or proteic reference sequences provided in a
FASTA file.
Grinder can produce genomic, metagenomic, transcriptomic, metatranscriptomic,
proteomic, metaproteomic shotgun and amplicon datasets from current
sequencing technologies such as Sanger, 454, Illumina. These simulated
datasets can be used to test the accuracy of bioinformatic tools under
specific hypothesis, e.g. with or without sequencing errors, or with low or
high community diversity. Grinder may also be used to help decide between
alternative sequencing methods for a sequence-based project, e.g. should the
library be paired-end or not, how many reads should be sequenced.
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gromacs
Molecular dynamics simulator, with building and analysis tools
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Versions of package gromacs |
Release | Version | Architectures |
sid | 2024.4-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
trixie | 2024.4-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
experimental | 2025.0~beta-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bookworm | 2022.5-2 | amd64,arm64,mips64el,ppc64el,s390x |
stretch | 2016.1-2 | amd64,arm64,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2019.1-1 | amd64,arm64,armhf,i386 |
jessie | 5.0.2-1 | amd64,armel,armhf,i386 |
bullseye | 2020.6-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 2025.0~beta |
Debtags of package gromacs: |
field | biology, biology:structural, chemistry |
interface | commandline, x11 |
role | program |
uitoolkit | xlib |
x11 | application |
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License: DFSG free
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GROMACS is a versatile package to perform molecular dynamics, i.e. simulate
the Newtonian equations of motion for systems with hundreds to millions of
particles.
It is primarily designed for biochemical molecules like proteins and lipids
that have a lot of complicated bonded interactions, but since GROMACS is
extremely fast at calculating the nonbonded interactions (that usually
dominate simulations) many groups are also using it for research on non-
biological systems, e.g. polymers.
This package contains variants both for execution on a single machine, and
using the MPI interface across multiple machines.
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gsort
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Versions of package gsort |
Release | Version | Architectures |
sid | 0.1.4-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.1.4-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.1.4-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.1.4-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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gsort is a tool to sort genomic files according to a genomefile.
For example, to sort VCF to have order:
X, Y, 2, 1, 3, ... and the header needs to be kept at the top.
As a more likely example, if a file nneds to be sorted to match GATK
order (1 ... X, Y, MT) which is not possible with any other sorting
tool. With gsort one can simply place MT as the last chrom in the
".genome" file.
It will also be useful for getting files ready for use in bedtools.
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gubbins
phylogenetic analysis of genome sequences
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Versions of package gubbins |
Release | Version | Architectures |
bullseye | 2.4.1-4 | amd64,i386 |
bookworm | 2.4.1-5 | amd64,i386 |
trixie | 3.4-1 | amd64,i386 |
sid | 3.4-1 | amd64,i386 |
stretch | 2.2.0-1 | amd64,i386 |
buster | 2.3.4-1 | amd64,i386 |
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License: DFSG free
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Gubbins supports rapid phylogenetic analysis of large samples of
recombinant bacterial whole genome sequences.
Gubbins (Genealogies Unbiased By recomBinations In Nucleotide
Sequences) is an algorithm that iteratively identifies loci containing
elevated densities of base substitutions while concurrently constructing
a phylogeny based on the putative point mutations outside of these
regions. Simulations demonstrate the algorithm generates highly accurate
reconstructions under realistic models of short-term bacterial
evolution, and can be run in only a few hours on alignments of hundreds
of bacterial genome sequences.
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gwama
Genome-Wide Association Meta Analysis
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Versions of package gwama |
Release | Version | Architectures |
sid | 2.2.2+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 2.2.2+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.2.2+dfsg-2 | amd64,arm64,armhf,i386 |
bullseye | 2.2.2+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.2.2+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.2.2+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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GWAMA (Genome-Wide Association Meta Analysis) software performs
meta-analysis of the results of GWA studies of binary or
quantitative phenotypes. Fixed- and random-effect meta-analyses are
performed for both directly genotyped and imputed SNPs using
estimates of the allelic odds ratio and 95% confidence interval for
binary traits, and estimates of the allelic effect size and standard
error for quantitative phenotypes. GWAMA can be used for analysing
the results of all different genetic models (multiplicative,
additive, dominant, recessive). The software incorporates error
trapping facilities to identify strand alignment errors and allele
flipping, and performs tests of heterogeneity of effects between studies.
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harvest-tools
archiving and postprocessing for reference-compressed genomic multi-alignments
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Versions of package harvest-tools |
Release | Version | Architectures |
bookworm | 1.3-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.3-4 | amd64,arm64,armhf,i386 |
bullseye | 1.3-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.3-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.3-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.3-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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HarvestTools is a utility for creating and interfacing with Gingr files,
which are efficient archives that the Harvest Suite uses to store
reference-compressed multi-alignments, phylogenetic trees, filtered
variants and annotations. Though designed for use with Parsnp and Gingr,
HarvestTools can also be used for generic conversion between standard
bioinformatics file formats.
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hhsuite
sensitive protein sequence searching based on HMM-HMM alignment
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Versions of package hhsuite |
Release | Version | Architectures |
stretch | 3.0~beta2+dfsg-3 | amd64 |
bullseye | 3.3.0+ds-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
buster | 3.0~beta3+dfsg-3 | amd64 |
jessie | 2.0.16-5 | amd64 |
sid | 3.3.0+ds-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
trixie | 3.3.0+ds-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
bookworm | 3.3.0+ds-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
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License: DFSG free
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HH-suite is an open-source software package for sensitive protein sequence
searching based on the pairwise alignment of hidden Markov models (HMMs).
This package contains HHsearch and HHblits among other programs and utilities.
HHsearch takes as input a multiple sequence alignment (MSA) or profile HMM
and searches a database of HMMs (e.g. PDB, Pfam, or InterPro) for homologous
proteins. HHsearch is often used for protein structure prediction to detect
homologous templates and to build highly accurate query-template pairwise
alignments for homology modeling.
HHblits can build high-quality MSAs starting from single sequences or from
MSAs. It transforms these into a query HMM and, using an iterative search
strategy, adds significantly similar sequences from the previous search to
the updated query HMM for the next search iteration. Compared to PSI-BLAST,
HHblits is faster, up to twice as sensitive and produces more accurate
alignments.
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hilive
realtime alignment of Illumina reads
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Versions of package hilive |
Release | Version | Architectures |
buster | 1.1-2 | amd64,arm64,armhf |
bullseye | 2.0a-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 0.3-2 | amd64,arm64,armel,i386,mips64el,mipsel,ppc64el |
bookworm | 2.0a-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.0a-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
experimental | 2.0a-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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HiLive is a read mapping tool that maps Illumina HiSeq (or comparable)
reads to a reference genome right in the moment when they are produced.
This means, read mapping is finished as soon as the sequencer is
finished generating the data.
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hisat2
graph-based alignment of short nucleotide reads to many genomes
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Versions of package hisat2 |
Release | Version | Architectures |
trixie | 2.2.1-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.2.1-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 2.0.5-1 | amd64 |
buster | 2.1.0-2 | amd64 |
bullseye | 2.2.1-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.2.1-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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HISAT2 is a fast and sensitive alignment program for mapping next-generation
sequencing reads (both DNA and RNA) to a population of human genomes (as well
as against a single reference genome). Based on an extension of BWT for graphs
a graph FM index (GFM) was designed and implementd. In addition to using
one global GFM index that represents a population of human genomes, HISAT2
uses a large set of small GFM indexes that collectively cover the whole genome
(each index representing a genomic region of 56 Kbp, with 55,000 indexes
needed to cover the human population). These small indexes (called local
indexes), combined with several alignment strategies, enable rapid and
accurate alignment of sequencing reads. This new indexing scheme is called a
Hierarchical Graph FM index (HGFM).
The package is enhanced by the following packages:
multiqc
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hmmer
profile hidden Markov models for protein sequence analysis
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Versions of package hmmer |
Release | Version | Architectures |
bullseye | 3.3.2+dfsg-1 | amd64,i386 |
bookworm | 3.3.2+dfsg-1 | amd64,i386 |
stretch | 3.1b2+dfsg-5 | amd64,i386 |
sid | 3.4+dfsg-2 | amd64,arm64,i386 |
jessie | 3.1b1-3 | amd64,armel,armhf,i386 |
buster | 3.2.1+dfsg-1 | amd64,i386 |
trixie | 3.4+dfsg-2 | amd64,arm64,i386 |
Debtags of package hmmer: |
biology | format:aln, peptidic |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | searching |
works-with | db |
works-with-format | plaintext |
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License: DFSG free
|
HMMER is an implementation of profile hidden Markov model methods for
sensitive searches of biological sequence databases using multiple sequence
alignments as queries.
Given a multiple sequence alignment as input, HMMER builds a statistical
model called a "hidden Markov model" which can then be used as a query into
a sequence database to find (and/or align) additional homologues of the
sequence family.
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hmmer2
profile hidden Markov models for protein sequence analysis
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Versions of package hmmer2 |
Release | Version | Architectures |
jessie | 2.3.2-8 | amd64,armel,armhf,i386 |
buster | 2.3.2+dfsg-6 | amd64,arm64,armhf,i386 |
bullseye | 2.3.2+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.3.2+dfsg-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.3.2+dfsg-12 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.3.2+dfsg-12 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 2.3.2-13 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch-backports | 2.3.2+dfsg-6~bpo9+1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
HMMER is an implementation of profile hidden Markov model methods for
sensitive searches of biological sequence databases using multiple sequence
alignments as queries.
Given a multiple sequence alignment as input, HMMER builds a statistical
model called a "hidden Markov model" which can then be used as a query into
a sequence database to find (and/or align) additional homologues of the
sequence family.
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hyphy-mpi
Hypothesis testing using Phylogenies (MPI version)
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Versions of package hyphy-mpi |
Release | Version | Architectures |
stretch | 2.2.7+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 2.5.63+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 2.5.28+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.3.14+dfsg-1 | amd64,arm64,armhf,i386 |
bookworm | 2.5.47+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.5.63+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 2.5.65 |
|
License: DFSG free
|
HyPhy is an open-source software package for the analysis of genetic
sequences using techniques in phylogenetics, molecular evolution, and
machine learning. It features a complete graphical user interface (GUI)
and a rich scripting language for limitless customization of analyses.
Additionally, HyPhy features support for parallel computing environments
(via message passing interface) and it can be compiled as a shared
library and called from other programming environments such as Python or
R. Continued development of HyPhy is currently supported in part by an
NIGMS R01 award 1R01GM093939.
This package provides an executable using MPI to do multiprocessing.
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hyphy-pt
Hypothesis testing using Phylogenies (pthreads version)
|
Versions of package hyphy-pt |
Release | Version | Architectures |
bookworm | 2.5.47+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 2.2.7+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2.5.63+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 2.5.63+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 2.5.28+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.3.14+dfsg-1 | amd64,arm64,armhf,i386 |
upstream | 2.5.65 |
|
License: DFSG free
|
HyPhy is an open-source software package for the analysis of genetic
sequences using techniques in phylogenetics, molecular evolution, and
machine learning. It features a complete graphical user interface (GUI)
and a rich scripting language for limitless customization of analyses.
Additionally, HyPhy features support for parallel computing environments
(via message passing interface) and it can be compiled as a shared
library and called from other programming environments such as Python or
R. Continued development of HyPhy is currently supported in part by an
NIGMS R01 award 1R01GM093939.
This package provides an executable using pthreads to do multiprocessing.
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|
idba
iterative De Bruijn Graph short read assemblers
|
Versions of package idba |
Release | Version | Architectures |
sid | 1.1.3-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.1.3-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.1.2-1 | amd64,armel,armhf,i386 |
buster | 1.1.3-3 | amd64,arm64,armhf,i386 |
bullseye | 1.1.3-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.1.3-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.1.3-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
IDBA stands for iterative de Bruijn graph assembler. In computational
sequence biology, an assembler solves the puzzle coming from large
sequencing machines that feature many gigabytes of short reads from a
large genome.
This package provides several flavours of the IDBA assembler, as they all
share the same source tree but serve different purposes and evolved over time.
IDBA is the basic iterative de Bruijn graph assembler for
second-generation sequencing reads. IDBA-UD, an extension of IDBA,
is designed to utilize paired-end reads to assemble low-depth regions
and use progressive depth on contigs to reduce errors in high-depth
regions. It is a generic purpose assembler and especially good for
single-cell and metagenomic sequencing data. IDBA-Hybrid is another
update version of IDBA-UD, which can make use of a similar reference
genome to improve assembly result. IDBA-Tran is an iterative de Bruijn
graph assembler for RNA-Seq data.
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igblast
Immunoglobulin and T cell receptor variable domain sequence analysis
|
Versions of package igblast |
Release | Version | Architectures |
trixie | 1.19.0-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.19.0-1 | amd64,arm64,mips64el,ppc64el,s390x |
sid | 1.19.0-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
upstream | 1.22.0 |
|
License: DFSG free
|
IgBLAST allows users to view the matches to the germline V, D, and J
genes, details at rearrangement junctions, the delineation of IG V
domain framework regions, and complementarity determining regions.
IgBLAST has the capability to analyse nucleotide and protein
sequences, and can process sequences in batches. Furthermore,
IgBLAST allows searches against the germline gene databases and other
sequence databases simultaneously to minimize the chance of missing
possibly the best matching germline V gene.
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igor
infers V(D)J recombination processes from sequencing data
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Versions of package igor |
Release | Version | Architectures |
trixie | 1.4.0+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.3.0+dfsg-1 | amd64,arm64,armhf,i386 |
bullseye | 1.4.0+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.4.0+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.4.0+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
|
IGoR (Inference and Generation of Repertoires) is a versatile software
to analyze and model immune receptors generation, selection, mutation
and all other processes.
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igv
Integrative Genomics Viewer
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Versions of package igv |
Release | Version | Architectures |
jessie | 2.3.38+dfsg-1 (non-free) | all |
sid | 2.18.5+dfsg-1 | all |
bullseye | 2.6.3+dfsg-3 (non-free) | all |
trixie | 2.18.5+dfsg-1 | all |
bookworm | 2.16.0+dfsg-1 | all |
stretch | 2.3.90+dfsg-1 (non-free) | all |
upstream | 2.19.1 |
Debtags of package igv: |
field | biology |
interface | x11 |
network | client |
role | program |
scope | utility |
use | viewing |
works-with | biological-sequence |
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License: DFSG free
|
The Integrative Genomics Viewer (IGV) is a high-performance viewer that
efficiently handles large heterogeneous data sets, while providing a
smooth and intuitive user experience at all levels of genome resolution.
A key characteristic of IGV is its focus on the integrative nature of
genomic studies, with support for both array-based and next-generation
sequencing data, and the integration of clinical and phenotypic data.
Although IGV is often used to view genomic data from public sources,
its primary emphasis is to support researchers who wish to visualize and
explore their own data sets or those from colleagues. To that end, IGV
supports flexible loading of local and remote data sets, and is
optimized to provide high-performance data visualization and exploration
on standard desktop systems.
Please cite:
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz and Jill P Mesirov:
Integrative genomics viewer.
(PubMed,eprint)
Nature Biotechnology
29(1):24–26
(2011)
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indelible
powerful and flexible simulator of biological evolution
|
Versions of package indelible |
Release | Version | Architectures |
stretch | 1.03-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.03-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.03-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.03-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.03-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.03-4 | amd64,arm64,armhf,i386 |
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License: DFSG free
|
INDELible is a new, portable, and flexible application for biological
sequence simulation that combines many features in the same place for
the first time. Using a length-dependent model of indel formation it
can simulate evolution of multi-partitioned nucleotide, amino-acid,
or codon data sets through the processes of insertion, deletion, and
substitution in continuous time.
Nucleotide simulations may use the general unrestricted model or the
general time reversible model and its derivatives, and amino-acid
simulations can be conducted using fifteen different empirical rate
matrices. Substitution rate heterogeneity can be modeled via the
continuous and discrete gamma distributions, with or without a proportion
of invariant sites. INDELible can also simulate under non-homogeneous
and non-stationary conditions where evolutionary models are permitted
to change across a phylogeny.
Unique among indel simulation programs, INDELible offers the ability
to simulate using codon models that exhibit nonsynonymous/synonymous
rate ratio heterogeneity among sites and/or lineages.
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infernal
inference of RNA secondary structural alignments
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Versions of package infernal |
Release | Version | Architectures |
sid | 1.1.5-3 | amd64,arm64,i386 |
stretch | 1.1.2-1 | amd64,i386 |
buster | 1.1.2-2 | amd64,i386 |
bullseye | 1.1.4-1 | amd64,i386 |
jessie | 1.1.1-2 | amd64,i386 |
bookworm | 1.1.4-1 | amd64,i386 |
trixie | 1.1.5-3 | amd64,arm64,i386 |
Debtags of package infernal: |
biology | nuceleic-acids |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
use | analysing |
|
License: DFSG free
|
Infernal ("INFERence of RNA ALignment") searches DNA sequence
databases for RNA structure and sequence similarities. It provides an
implementation of a special variant of profile stochastic context-free
grammars called covariance models (CMs). A CM is like a sequence
profile, but it scores a combination of sequence consensus and RNA
secondary structure consensus, so in many cases, it is more capable of
identifying RNA homologs that conserve their secondary structure more
than their primary sequence.
The tool is an integral component of the Rfam database.
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insilicoseq
sequencing simulator producing realistic Illumina reads
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Versions of package insilicoseq |
Release | Version | Architectures |
trixie | 2.0.1-1 | all |
bookworm | 1.5.4-6 | all |
sid | 2.0.1-1 | all |
bullseye | 1.5.2-1 | all |
|
License: DFSG free
|
Primarily intended for simulating metagenomic samples, it can also be
used to produce sequencing data from a single genome.
InSilicoSeq is written in Python, and use kernel density estimators to
model the read quality of real sequencing data.
InSilicoSeq support substitution, insertion and deletion errors. If
you don't have the use for insertion and deletion error a basic
error model is provided.
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ipig
integrating PSMs into genome browser visualisations
|
Versions of package ipig |
Release | Version | Architectures |
trixie | 0.0.r5-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 0.0.r5-1 | amd64,armel,armhf,i386 |
stretch | 0.0.r5-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.0.r5-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.0.r5-3 | amd64,arm64,armhf,i386 |
bullseye | 0.0.r5-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.0.r5-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
iPiG targets the integration of peptide spectrum matches (PSMs) from
mass spectrometry (MS) peptide identifications into genomic
visualisations provided by genome browser such as the UCSC genome
browser (http://genome.ucsc.edu/).
iPiG takes PSMs from the MS standard format mzIdentML (*.mzid) or in
text format and provides results in genome track formats (BED and GFF3
files), which can be easily imported into genome browsers.
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iqtree
efficient phylogenetic software by maximum likelihood
|
Versions of package iqtree |
Release | Version | Architectures |
bullseye | 1.6.12+dfsg-1 | amd64,i386 |
buster | 1.6.9+dfsg-1 | amd64,i386 |
bookworm | 2.0.7+dfsg-1 | amd64,i386 |
sid | 2.0.7+dfsg-1 | amd64,i386 |
trixie | 2.0.7+dfsg-1 | amd64,i386 |
stretch | 1.5.3+dfsg-2 | amd64,i386 |
|
License: DFSG free
|
IQ-TREE is a very efficient maximum likelihood phylogenetic software
with following key features among others:
- A novel fast and effective stochastic algorithm to estimate maximum
likelihood trees. IQ-TREE outperforms both RAxML and PhyML in terms
of likelihood while requiring similar amount of computing time (see
Nguyen et al., 2015)
- An ultrafast bootstrap approximation to assess branch supports (see
Minh et al., 2013).
- A wide range of substitution models for binary, DNA, protein, codon,
and morphological alignments.
- Ultrafast model selection for all data types, 10 to 100 times faster
than jModelTest and ProtTest.
- Finding best partition scheme like PartitionFinder.
- Partitioned models with mixed data types for phylogenomic (multi-
gene) alignments, allowing for separate, proportional, or joint
branch lengths among genes.
- Supporting the phylogenetic likelihod library (PLL) (see Flouri et
al., 2014)
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iva
iterative virus sequence assembler
|
Versions of package iva |
Release | Version | Architectures |
bookworm | 1.0.11+ds-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
bullseye | 1.0.9+ds-11 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
trixie | 1.0.11+ds-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
sid | 1.0.11+ds-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
buster | 1.0.9+ds-6 | amd64,arm64 |
stretch | 1.0.8+ds-1 | amd64,arm64,mips64el,ppc64el |
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License: DFSG free
|
IVA is a de novo assembler designed to assemble
virus genomes that have no repeat sequences,
using Illumina read pairs sequenced from mixed
populations at extremely high depth.
IVA's main algorithm works by iteratively extending
contigs using aligned read pairs. Its input can be
just read pairs, or additionally you can provide an
existing set of contigs to be extended. Alternatively,
it can take reads together with a reference sequence.
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jaligner
Smith-Waterman algorithm with Gotoh's improvement
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Versions of package jaligner |
Release | Version | Architectures |
bookworm | 1.0+dfsg-10 | all |
sid | 1.0+dfsg-11 | all |
bullseye | 1.0+dfsg-7 | all |
buster | 1.0+dfsg-6 | all |
stretch | 1.0+dfsg-4 | all |
trixie | 1.0+dfsg-11 | all |
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License: DFSG free
|
JAligner is an open source Java implementation of the Smith-Waterman
algorithm with Gotoh's improvement for biological local pairwise sequence
alignment with the affine gap penalty model.
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jalview
multiple alignment editor
|
Versions of package jalview |
Release | Version | Architectures |
trixie | 2.11.4.0+dfsg-3 | all |
bookworm | 2.11.2.5+dfsg-3 | all |
jessie | 2.7.dfsg-4 | all |
sid | 2.11.4.0+dfsg-3 | all |
bullseye | 2.11.1.3+dfsg2-5 | all |
upstream | 2.11.4.1 |
|
License: DFSG free
|
JalView is a Java DNA, RNA and protein sequence alignment editor that can work
with sequence alignments produced by programs implementing alignment
algorithms such as clustalw, kalign and t-coffee.
It has lots of features, is actively developed, and will compare
advantageously to BioEdit, while being free as in free speech!
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jellyfish
count k-mers in DNA sequences
|
Versions of package jellyfish |
Release | Version | Architectures |
jessie | 2.1.4-1 | amd64 |
stretch | 2.2.6-1 | amd64 |
buster | 2.2.10-2 | amd64,arm64 |
sid | 2.3.1-4 | amd64,arm64,mips64el,ppc64el,riscv64 |
trixie | 2.3.1-4 | amd64,arm64,mips64el,ppc64el,riscv64 |
bookworm | 2.3.0-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el |
bullseye | 2.3.0-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el |
|
License: DFSG free
|
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
DNA. A k-mer is a substring of length k, and counting the occurrences
of all such substrings is a central step in many analyses of DNA
sequence. JELLYFISH can count k-mers using an order of magnitude less
memory and an order of magnitude faster than other k-mer counting
packages by using an efficient encoding of a hash table and by
exploiting the "compare-and-swap" CPU instruction to increase
parallelism.
JELLYFISH is a command-line program that reads FASTA and multi-FASTA
files containing DNA sequences. It outputs its k-mer counts in an
binary format, which can be translated into a human-readable text
format using the "jellyfish dump" command.
The package is enhanced by the following packages:
multiqc
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jellyfish1
count k-mers in DNA sequences
|
Versions of package jellyfish1 |
Release | Version | Architectures |
bookworm | 1.1.11-8 | amd64,arm64,mips64el,ppc64el |
bullseye | 1.1.11-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x |
sid | 1.1.11-10 | amd64,arm64,mips64el,ppc64el,riscv64 |
buster | 1.1.11-4 | amd64,arm64,armhf,i386 |
stretch-backports | 1.1.11-3~bpo9+1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x |
trixie | 1.1.11-9 | amd64,arm64,mips64el,ppc64el,riscv64 |
|
License: DFSG free
|
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
DNA. A k-mer is a substring of length k, and counting the occurrences
of all such substrings is a central step in many analyses of DNA
sequence. JELLYFISH can count k-mers using an order of magnitude less
memory and an order of magnitude faster than other k-mer counting
packages by using an efficient encoding of a hash table and by
exploiting the "compare-and-swap" CPU instruction to increase
parallelism.
JELLYFISH is a command-line program that reads FASTA and multi-FASTA
files containing DNA sequences. It outputs its k-mer counts in an
binary format, which can be translated into a human-readable text
format using the "jellyfish dump" command.
This is the latest version of the 1.x series of jellyfish which is
used by some other applications that are not compatible with version
2.x which is provided inside the jellyfish package.
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jmodeltest
HPC selection of models of nucleotide substitution
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Versions of package jmodeltest |
Release | Version | Architectures |
bookworm | 2.1.10+dfsg-12 | all |
sid | 2.1.10+dfsg-12 | all |
bullseye | 2.1.10+dfsg-10 | all |
buster | 2.1.10+dfsg-7 | all |
stretch | 2.1.10+dfsg-5 | all |
trixie | 2.1.10+dfsg-12 | all |
|
License: DFSG free
|
jModelTest is a tool to carry out statistical selection of best-fit
models of nucleotide substitution. It implements five different model
selection strategies: hierarchical and dynamical likelihood ratio tests
(hLRT and dLRT), Akaike and Bayesian information criteria (AIC and BIC),
and a decision theory method (DT). It also provides estimates of model
selection uncertainty, parameter importances and model-averaged
parameter estimates, including model-averaged tree topologies.
jModelTest 2 includes High Performance Computing (HPC) capabilities and
additional features like new strategies for tree optimization, model-
averaged phylogenetic trees (both topology and branch length), heuristic
filtering and automatic logging of user activity.
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jmol
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Versions of package jmol |
Release | Version | Architectures |
buster | 14.6.4+2016.11.05+dfsg1-4 | all |
stretch | 14.6.4+2016.11.05+dfsg1-3 | all |
bullseye | 14.6.4+2016.11.05+dfsg1-4 | all |
sid | 16.2.33+dfsg-1 | all |
bookworm | 14.32.83+dfsg-2 | all |
jessie | 12.2.32+dfsg2-1 | all |
trixie | 16.2.33+dfsg-1 | all |
upstream | 16.2.37 |
Debtags of package jmol: |
field | chemistry |
role | program |
scope | utility |
use | viewing |
|
License: DFSG free
|
Jmol is a Java molecular viewer for three-dimensional chemical structures.
Features include reading a variety of file types and output from quantum
chemistry programs, and animation of multi-frame files and computed normal
modes from quantum programs. It includes with features for chemicals,
crystals, materials and biomolecules. Jmol might be useful for students,
educators, and researchers in chemistry and biochemistry.
File formats read by Jmol include PDB, XYZ, CIF, CML, MDL Molfile, Gaussian,
GAMESS, MOPAC, ABINIT, ACES-II, Dalton and VASP.
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kalign
Global and progressive multiple sequence alignment
|
Versions of package kalign |
Release | Version | Architectures |
stretch | 2.03+20110620-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.03+20110620-5 | amd64,arm64,armhf,i386 |
jessie | 2.03+20110620-2 | amd64,armel,armhf,i386 |
bookworm | 3.3.5-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 3.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 3.4.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 3.4.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package kalign: |
biology | format:aln, nuceleic-acids, peptidic |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | comparing |
works-with-format | plaintext |
|
License: DFSG free
|
Kalign is a command line tool to perform multiple alignment of
biological sequences. It employs the Muth-Manber string-matching
algorithm, to improve both the accuracy and speed of the alignment.
It uses global, progressive alignment approach, enriched by employing
an approximate string-matching algorithm to calculate sequence
distances and by incorporating local matches into the otherwise global
alignment.
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kallisto
near-optimal RNA-Seq quantification
|
Versions of package kallisto |
Release | Version | Architectures |
sid | 0.48.0+dfsg-4 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.46.2+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.48.0+dfsg-3 | amd64,arm64,mips64el,ppc64el,s390x |
trixie | 0.48.0+dfsg-4 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
upstream | 0.51.1 |
|
License: DFSG free
|
Kallisto is a program for quantifying abundances of transcripts from
RNA-Seq data, or more generally of target sequences using high-throughput
sequencing reads. It is based on the novel idea of pseudoalignment for
rapidly determining the compatibility of reads with targets, without the
need for alignment. On benchmarks with standard RNA-Seq data, kallisto
can quantify 30 million human reads in less than 3 minutes on a Mac
desktop computer using only the read sequences and a transcriptome index
that itself takes less than 10 minutes to build. Pseudoalignment of
reads preserves the key information needed for quantification, and
kallisto is therefore not only fast, but also as accurate than existing
quantification tools. In fact, because the pseudoalignment procedure is
robust to errors in the reads, in many benchmarks kallisto significantly
outperforms existing tools.
The package is enhanced by the following packages:
multiqc
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kaptive
obtain information about K and O types for Klebsiella genome assemblies
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Versions of package kaptive |
Release | Version | Architectures |
buster-backports | 0.7.0-2~bpo10+1 | all |
bookworm | 2.0.4-1 | all |
trixie | 2.0.8-1 | all |
stretch-backports-sloppy | 0.7.0-2~bpo9+1 | all |
bullseye | 0.7.3-3 | all |
sid | 2.0.8-1 | all |
upstream | 3.0.0b6 |
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License: DFSG free
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Kaptive reports information about K and O types for Klebsiella genome
assemblies.
Given a novel genome and a database of known loci (K or O), Kaptive will
help a user to decide whether their sample has a known or novel locus.
It carries out the following for each input assembly:
- BLAST for all known locus nucleotide sequences (using blastn) to
identify the best match ('best' defined as having the highest
coverage).
- Extract the region(s) of the assembly which correspond to the BLAST
hits (i.e. the locus sequence in the assembly) and save it to a
FASTA file.
- BLAST for all known locus genes (using tblastn) to identify which
expected genes (genes in the best matching locus) are present/missing
and whether any unexpected genes (genes from other loci) are present.
- Output a summary to a table file.
In cases where your input assembly closely matches a known locus,
Kaptive should make that obvious. When your assembly has a novel type,
that too should be clear. However, Kaptive cannot reliably extract or
annotate locus sequences for totally novel types - if it indicates a
novel locus is present then extracting and annotating the sequence is up
to you! Very poor assemblies can confound the results, so be sure to
closely examine any case where the locus sequence in your assembly is
broken into multiple pieces.
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khmer
in-memory DNA sequence kmer counting, filtering & graph traversal
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Versions of package khmer |
Release | Version | Architectures |
bookworm | 3.0.0~a3+dfsg-4 | amd64 |
stretch | 2.0+dfsg-10 | amd64,arm64,mips64el,ppc64el |
sid | 3.0.0~a3+dfsg-8 | amd64 |
buster | 2.1.2+dfsg-6 | amd64,arm64 |
experimental | 3.0.0~a3+dfsg-9~0exp | amd64 |
bullseye | 2.1.2+dfsg-8 | amd64,arm64 |
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License: DFSG free
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khmer is a library and suite of command line tools for working with DNA
sequence. It is primarily aimed at short-read sequencing data such as that
produced by the Illumina platform. khmer takes a k-mer-centric approach to
sequence analysis, hence the name.
Please cite:
Michael R. Crusoe, Hussien F. Alameldin, Sherine Awad, Elmar Bucher, Adam Caldwell, Reed Cartwright, Amanda Charbonneau, Bede Constantinides, Greg Edvenson, Scott Fay, Jacob Fenton, Thomas Fenzl, Jordan Fish, Leonor Garcia-Gutierrez, Phillip Garland, Jonathan Gluck, Iván González, Sarah Guermond, Jiarong Guo, Aditi Gupta, Joshua R. Herr, Adina Howe, Alex Hyer, Andreas Härpfer, Luiz Irber, Rhys Kidd, David Lin, Justin Lippi, Tamer Mansour, Pamela McA'Nulty, Eric McDonald, Jessica Mizzi, Kevin D. Murray, Joshua R. Nahum, Kaben Nanlohy, Alexander Johan Nederbragt, Humberto Ortiz-Zuazaga, Jeramia Ory, Jason Pell, Charles Pepe-Ranney, Zachary N Russ, Erich Schwarz, Camille Scott, Josiah Seaman, Scott Sievert, Jared Simpson, Connor T. Skennerton, James Spencer, Ramakrishnan Srinivasan, Daniel Standage, James A. Stapleton, Joe Stein, Susan R Steinman, Benjamin Taylor, Will Trimble, Heather L. Wiencko, Michael Wright, Brian Wyss, Qingpeng Zhang, en zyme and C. Titus Brown:
The khmer software package: enabling efficient sequence analysis.
(2015)
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kineticstools
detection of DNA modifications
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Versions of package kineticstools |
Release | Version | Architectures |
buster | 0.6.1+git20180425.27a1878-2 | all |
sid | 0.6.1+git20220223.1326a4d+dfsg-3 | all |
trixie | 0.6.1+git20220223.1326a4d+dfsg-3 | all |
bookworm | 0.6.1+git20220223.1326a4d+dfsg-2 | all |
stretch | 0.6.1+20161222-1 | all |
bullseye | 0.6.1+git20200729.e3723e0+dfsg-1 | all |
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License: DFSG free
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Tools for detecting DNA modifications from single molecule, real-time (SMRT®)
sequencing data. This tool implements the P_ModificationDetection module in
SMRT® Portal, used by the RS_Modification_Detection and
RS_Modifications_and_Motif_Detection protocol. Researchers interested in
understanding or extending the modification detection algorithms can use these
tools as a starting point.
This package is part of the SMRTAnalysis suite.
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king-probe
Evaluate and visualize protein interatomic packing
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Versions of package king-probe |
Release | Version | Architectures |
trixie | 02.21-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 02.21-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 02.21-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.16.160404+git20200121.9b198c1-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.16.160404+git20180613.a09b012-1 | amd64,arm64,armhf,i386 |
stretch | 2.13.110909-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
upstream | 02.26 |
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License: DFSG free
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king-probe is a program that allows one to evaluate atomic packing, either
within or between molecules. It generates "contact dots" where
atoms are in close contact.
The program king-probe generates "contact dots" at points on the van der
Waals surface of atoms which are in close proximity to other atoms; reading
atomic coordinates in protein databank (PDB) format files and writing
color-coded dot lists (spikes where atoms clash) for inclusion in a
kinemage.
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kissplice
Detection of various kinds of polymorphisms in RNA-seq data
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Versions of package kissplice |
Release | Version | Architectures |
stretch | 2.4.0-p1-1 | amd64,arm64,mips64el,ppc64el |
buster | 2.4.0-p1-4 | amd64,arm64 |
sid | 2.6.7-1 | amd64,arm64,mips64el,ppc64el,riscv64 |
bullseye | 2.5.3-3 | amd64,arm64,mips64el,ppc64el |
jessie | 2.2.1-3 | amd64 |
bookworm | 2.6.2-2 | amd64,arm64,mips64el,ppc64el |
trixie | 2.6.7-1 | amd64,arm64,mips64el,ppc64el,riscv64 |
Debtags of package kissplice: |
biology | nuceleic-acids |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
use | analysing |
works-with | biological-sequence |
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License: DFSG free
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KisSplice is a piece of software that enables the analysis of RNA-seq data
with or without a reference genome. It is an exact local transcriptome
assembler that allows one to identify SNPs, indels and alternative splicing
events. It can deal with an arbitrary number of biological conditions, and
will quantify each variant in each condition.
It has been tested on Illumina datasets of up to 1G reads.
Its memory consumption is around 5Gb for 100M reads.
Topics: RNA-seq; RNA splicing; Gene structure
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kleborate
tool to screen Klebsiella genome assemblies
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Versions of package kleborate |
Release | Version | Architectures |
buster-backports | 1.0.0-3~bpo10+1 | amd64,arm64,mips64el,ppc64el,s390x |
bookworm | 2.3.1-2 | amd64,arm64,mips64el,ppc64el,s390x |
bullseye | 2.0.1-1 | amd64,arm64,mips64el,ppc64el,s390x |
trixie | 2.4.1-3 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
stretch-backports-sloppy | 1.0.0-3~bpo9+1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
sid | 2.4.1-3 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
upstream | 3.1.2 |
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License: DFSG free
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Kleborate is a tool to screen Klebsiella genome assemblies for:
- MLST sequence type
- species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.)
- ICEKp associated virulence loci: yersiniabactin (ybt),
colibactin (clb)
- virulence plasmid associated loci: salmochelin (iro), aerobactin
(iuc), hypermucoidy (rmpA, rmpA2)
- antimicrobial resistance genes, including quinolone resistance SNPs
and colistin resistance truncations
- K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles
and Kaptive
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kma
mapping genomic sequences to raw reads directly against redundant databases
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Versions of package kma |
Release | Version | Architectures |
stretch-backports-sloppy | 1.2.21-1~bpo9+1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.4.15-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.4.11-1 | amd64,arm64,mips64el,ppc64el,s390x |
trixie | 1.4.15-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.3.10-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 1.4.17 |
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License: DFSG free
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KMA is mapping a method designed to map raw reads directly against
redundant databases, in an ultra-fast manner using seed and extend. KMA
is particularly good at aligning high quality reads against highly
redundant databases, where unique matches often does not exist. It works
for long low quality reads as well, such as those from Nanopore. Non-
unique matches are resolved using the "ConClave" sorting scheme, and a
consensus sequence are outputtet in addition to other common attributes.
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kmc
count kmers in genomic sequences
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Versions of package kmc |
Release | Version | Architectures |
stretch | 2.3+dfsg-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.2.1+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 3.2.4+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 3.1.1+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 3.2.4+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 2.3+dfsg-7 | amd64,arm64,armhf,i386 |
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License: DFSG free
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The kmc software is designed for counting k-mers (sequences of
consecutive k symbols) in a set of reads. K-mer counting is
important for many bioinformatics applications, e.g. developing de Bruijn
graph assemblers.
Building de Bruijn graphs is a commonly used approach for genome
assembly with data from second-generation sequencing.
Unfortunately, sequencing errors (frequent in practice)
result in huge memory requirements for de Bruijn graphs, as well
as long build time. One of the popular approaches to handle this
problem is filtering the input reads in such a way that unique k-mers
(very likely obtained as a result of an error) are discarded.
Thus, KMC scans the raw reads and produces a compact representation
of all non-unique reads accompanied with number of their occurrences.
The algorithm implemented in KMC makes use mostly of disk space rather
than RAM, which allows one to use KMC even on rather typical personal
computers. When run on high-end servers (what is necessary for KMC
competitors) it outperforms them in both memory requirements and
speed of computation. The disk space necessary for computation is in
order of the size of input data (usually it is smaller).
Topics: Sequence composition, complexity and repeats
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kmer
suite of tools for DNA sequence analysis
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Versions of package kmer |
Release | Version | Architectures |
buster | 0~20150903+r2013-6 | all |
sid | 0~20150903+r2013-9 | all |
stretch | 0~20150903+r2013-3 | all |
bookworm | 0~20150903+r2013-8 | all |
bullseye | 0~20150903+r2013-8 | all |
trixie | 0~20150903+r2013-9 | all |
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License: DFSG free
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The kmer package is a suite of tools for DNA sequence analysis.
It provides tools for searching (ESTs, mRNAs, sequencing reads);
aligning (ESTs, mRNAs, whole genomes); and a variety of analyses
based on kmers.
This is a metapackage depending on the executable components of the kmer suite.
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kmerresistance
correlates mapped genes with the predicted species of WGS samples
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Versions of package kmerresistance |
Release | Version | Architectures |
trixie | 2.2.0-4 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bullseye | 2.2.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.2.0-4 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.2.0-4 | amd64,arm64,mips64el,ppc64el,s390x |
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License: DFSG free
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KmerResistance correlates mapped genes with the predicted species of WGS
samples, where this allows for identification of genes in samples which
have been poorly sequenced or high accuracy predictions for samples with
contamination. KmerResistance has one dependency, namely KMA to perform
the mapping, which is also freely available.
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kraken
assigning taxonomic labels to short DNA sequences
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Versions of package kraken |
Release | Version | Architectures |
bookworm | 1.1.1-4 | amd64,arm64,mips64el,ppc64el |
bullseye | 1.1.1-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x |
stretch | 0.10.5~beta-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch-backports | 1.1-2~bpo9+1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x |
trixie | 1.1.1-4 | amd64,arm64,mips64el,ppc64el,riscv64 |
sid | 1.1.1-4 | amd64,arm64,mips64el,ppc64el,riscv64 |
buster | 1.1-3 | amd64,arm64,armhf,i386 |
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License: DFSG free
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Kraken is a system for assigning taxonomic labels to short DNA
sequences, usually obtained through metagenomic studies. Previous
attempts by other bioinformatics software to accomplish this task have
often used sequence alignment or machine learning techniques that were
quite slow, leading to the development of less sensitive but much faster
abundance estimation programs. Kraken aims to achieve high sensitivity
and high speed by utilizing exact alignments of k-mers and a novel
classification algorithm.
In its fastest mode of operation, for a simulated metagenome of 100 bp
reads, Kraken processed over 4 million reads per minute on a single
core, over 900 times faster than Megablast and over 11 times faster than
the abundance estimation program MetaPhlAn. Kraken's accuracy is
comparable with Megablast, with slightly lower sensitivity and very high
precision.
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kraken2
taxonomic classification system using exact k-mer matches
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Versions of package kraken2 |
Release | Version | Architectures |
bullseye | 2.1.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.1.3-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.1.3-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.1.2-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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Kraken 2 is the newest version of Kraken, a taxonomic classification
system using exact k-mer matches to achieve high accuracy and fast
classification speeds. This classifier matches each k-mer within a query
sequence to the lowest common ancestor (LCA) of all genomes containing
the given k-mer. The k-mer assignments inform the classification
algorithm. [see: Kraken 1's Webpage for more details].
Kraken 2 provides significant improvements to Kraken 1, with faster
database build times, smaller database sizes, and faster classification
speeds. These improvements were achieved by the following updates to the
Kraken classification program:
1. Storage of Minimizers: Instead of storing/querying entire k-mers,
Kraken 2 stores minimizers (l-mers) of each k-mer. The length of
each l-mer must be ≤ the k-mer length. Each k-mer is treated by
Kraken 2 as if its LCA is the same as its minimizer's LCA.
2. Introduction of Spaced Seeds: Kraken 2 also uses spaced seeds to
store and query minimizers to improve classification accuracy.
3. Database Structure: While Kraken 1 saved an indexed and sorted list
of k-mer/LCA pairs, Kraken 2 uses a compact hash table. This hash
table is a probabilistic data structure that allows for faster
queries and lower memory requirements. However, this data structure
does have a <1% chance of returning the incorrect LCA or returning
an LCA for a non-inserted minimizer. Users can compensate for this
possibility by using Kraken's confidence scoring thresholds.
4. Protein Databases: Kraken 2 allows for databases built from amino
acid sequences. When queried, Kraken 2 performs a six-frame
translated search of the query sequences against the database.
5. 16S Databases: Kraken 2 also provides support for databases not
based on NCBI's taxonomy. Currently, these include the 16S
databases: Greengenes, SILVA, and RDP.
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lagan
highly parametrizable pairwise global genome sequence aligner
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Versions of package lagan |
Release | Version | Architectures |
trixie | 2.0-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 2.0-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.0-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch-backports | 2.0-3~bpo9+1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.0-3 | amd64,arm64,armhf,i386 |
sid | 2.0-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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Lagan takes local alignments generated by CHAOS as anchors, and limits
the search area of the Needleman-Wunsch algorithm around these anchors.
Multi-LAGAN is a generalization of the pairwise algorithm to multiple
sequence alignment. M-LAGAN performs progressive pairwise alignments,
guided by a user-specified phylogenetic tree. Alignments are aligned to
other alignments using the sum-of-pairs metric.
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lamarc
Likelihood Analysis with Metropolis Algorithm using Random Coalescence
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Versions of package lamarc |
Release | Version | Architectures |
trixie | 2.1.10.1+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 2.1.10.1+dfsg-3 | amd64,arm64,armhf,i386 |
bullseye | 2.1.10.1+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.1.10.1+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.1.10.1+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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LAMARC is a program which estimates population-genetic parameters such
as population size, population growth rate, recombination rate, and
migration rates. It approximates a summation over all possible
genealogies that could explain the observed sample, which may be
sequence, SNP, microsatellite, or electrophoretic data. LAMARC and its
sister program Migrate are successor programs to the older programs
Coalesce, Fluctuate, and Recombine, which are no longer being supported.
The programs are memory-intensive but can run effectively on
workstations.
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lamassemble
Merges overlapping "long" DNA reads into a consensus sequences
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Versions of package lamassemble |
Release | Version | Architectures |
trixie | 1.7.2-2 | all |
bookworm | 1.4.2-5 | all |
sid | 1.7.2-2 | all |
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License: DFSG free
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lamassemble merges overlapping "long" DNA reads into a consensus
sequence (i.e. assembles them). It works OK when the number of reads
is less than a thousand or so.
The merging is not always accurate. In particular, if the reads come
from huge tandem repeats, wrong parts of the reads may get merged.
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lambda-align
Local Aligner for Massive Biological DatA
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Versions of package lambda-align |
Release | Version | Architectures |
stretch | 1.0.1-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
experimental | 1.0.3-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.0.3-5 | amd64,arm64,armhf,i386 |
bullseye | 1.0.3-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.0.3-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.0.3-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.0.3-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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Lambda is a local biosequence aligner optimized for many query sequences
and searches in protein space. It is compatible to the de facto standard tool
BLAST, but often outperforms the best currently available alternatives at
reproducing BLAST’s results and is the fastest compared with the current
state of the art at comparable levels of sensitivity.
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lambda-align2
Local Aligner for Massive Biological DatA - v2
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Versions of package lambda-align2 |
Release | Version | Architectures |
trixie | 2.0.1-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.0.0-9 | amd64 |
buster | 2.0.0-6 | amd64 |
bullseye | 2.0.0-9 | amd64 |
sid | 2.0.1-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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Lambda2 is a local biosequence aligner optimized for many query sequences
and searches in protein space. It is compatible to the de facto standard tool
BLAST, but often outperforms the best currently available alternatives at
reproducing BLAST’s results and is the fastest compared with the current
state of the art at comparable levels of sensitivity.
This package is for the Lambda (align) v2.x series which has an incompatible
command line interface and on disk format from Lambda (align) v1.x.
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last-align
genome-scale comparison of biological sequences
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Versions of package last-align |
Release | Version | Architectures |
buster | 963-2 | amd64,arm64,armhf,i386 |
bullseye | 1179-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1447-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1542-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1542-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 490-1 | amd64,armel,armhf,i386 |
stretch | 830-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package last-align: |
biology | nuceleic-acids |
field | biology, biology:bioinformatics |
role | program |
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License: DFSG free
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LAST is software for comparing and aligning sequences, typically DNA or
protein sequences. LAST is similar to BLAST, but it copes better with very
large amounts of sequence data. Here are two things LAST is good at:
- Comparing large (e.g. mammalian) genomes.
- Mapping lots of sequence tags onto a genome.
The main technical innovation is that LAST finds initial matches based on
their multiplicity, instead of using a fixed size (e.g. BLAST uses 10-mers).
This allows one to map tags to genomes without repeat-masking, without becoming
overwhelmed by repetitive hits. To find these variable-sized matches, it uses
a suffix array (inspired by Vmatch). To achieve high sensitivity, it uses a
discontiguous suffix array, analogous to spaced seeds.
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lastz
pairwise aligning DNA sequences
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Versions of package lastz |
Release | Version | Architectures |
trixie | 1.04.22-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.04.03-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.04.22-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.04.22-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 1.04.41 |
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License: DFSG free
|
LASTZ is a drop-in replacement for BLASTZ, and is backward compatible with
BLASTZ’s command-line syntax. That is, it supports all of BLASTZ’s options
but also has additional ones, and may produce slightly different alignment
results.
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leaff
biological sequence library utilities and applications
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Versions of package leaff |
Release | Version | Architectures |
stretch | 0~20150903+r2013-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 0~20150903+r2013-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0~20150903+r2013-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0~20150903+r2013-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0~20150903+r2013-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0~20150903+r2013-6 | amd64,arm64,armhf,i386 |
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License: DFSG free
|
LEAFF (Let's Extract Anything From Fasta) is a utility program for
working with multi-fasta files. In addition to providing random access
to the base level, it includes several analysis functions.
This package is part of the Kmer suite.
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lefse
determine features of organisms, clades, taxonomic units, genes
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Versions of package lefse |
Release | Version | Architectures |
sid | 1.1.2-2 | all |
buster | 1.0.8-2 | all |
trixie | 1.1.2-2 | all |
bookworm | 1.1.2-1 | all |
stretch | 1.0+20160802-1 | all |
bullseye | 1.0.8-3 | all |
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License: DFSG free
|
LEfSe (Linear discriminant analysis Effect Size) determines the features
(organisms, clades, operational taxonomic units, genes, or functions)
most likely to explain differences between classes by coupling standard
tests for statistical significance with additional tests encoding
biological consistency and effect relevance.
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libpwiz-tools
ProteoWizard command line tools
|
Versions of package libpwiz-tools |
Release | Version | Architectures |
jessie | 3.0.6585-2 | amd64,armel,armhf,i386 |
sid | 3.0.18342-4.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 3.0.9393-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 3.0.18342-2 | amd64,arm64,armhf,i386 |
bookworm | 3.0.18342-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 3.0.18342-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
The libpwiz library from the ProteoWizard project provides a modular
and extensible set of open-source, cross-platform tools and
libraries. The tools perform proteomics data analyses; the libraries
enable rapid tool creation by providing a robust, pluggable
development framework that simplifies and unifies data file access,
and performs standard chemistry and LCMS dataset computations.
The primary goal of ProteoWizard is to eliminate the existing
barriers to proteomic software development so that researchers can
focus on the development of new analytic approaches, rather than
having to dedicate significant resources to mundane (if important)
tasks, like reading data files.
This package ships command line tools that include idconvert
(conversion of MS identifications) and msconvert (conversion of MS
raw data files from/to any supported format).
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librg-utils-perl
parsers and format conversion utilities used by (e.g.) profphd
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Versions of package librg-utils-perl |
Release | Version | Architectures |
stretch | 1.0.43-4 | all |
buster | 1.0.43-6 | all |
trixie | 1.0.43-8 | all |
bullseye | 1.0.43-7 | all |
bookworm | 1.0.43-8 | all |
jessie | 1.0.43-2 | all |
sid | 1.0.43-9 | all |
Debtags of package librg-utils-perl: |
devel | lang:perl, library |
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License: DFSG free
|
This package contributes to the PredictProtein server for the automated
structural annotation of protein sequences. It features as series of conversion
tools like:
- blast2saf.pl
- blastpgp_to_saf.pl
- conv_hssp2saf.pl
- copf.pl
- hssp_filter.pl
- safFilterRed.pl
which are supported by the modules:
- RG:Utils::Conv_hssp2saf
- RG:Utils::Copf
- RG:Utils::Hssp_filter
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libvcflib-tools
C++ library for parsing and manipulating VCF files (tools)
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Versions of package libvcflib-tools |
Release | Version | Architectures |
trixie | 1.0.9+dfsg1-3 | amd64,arm64,mips64el,ppc64el,riscv64 |
stretch-backports | 1.0.0~rc1+dfsg1-6~bpo9+1 | amd64 |
bookworm | 1.0.3+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.0.9+dfsg1-3 | amd64,arm64,mips64el,ppc64el,riscv64 |
bullseye | 1.0.2+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.0~rc2+dfsg-2 | amd64 |
stretch | 1.0.0~rc1+dfsg1-3 | amd64 |
buster-backports | 1.0.1+dfsg-3~bpo10+1 | amd64 |
upstream | 1.0.12 |
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License: DFSG free
|
The Variant Call Format (VCF) is a flat-file, tab-delimited textual format
intended to concisely describe reference-indexed variations between
individuals. VCF provides a common interchange format for the description of
variation in individuals and populations of samples, and has become the defacto
standard reporting format for a wide array of genomic variant detectors.
vcflib provides methods to manipulate and interpret sequence variation as it
can be described by VCF. It is both:
- an API for parsing and operating on records of genomic variation as it can
be described by the VCF format,
- and a collection of command-line utilities for executing complex
manipulations on VCF files.
This package contains several tools using the library.
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lighter
fast and memory-efficient sequencing error corrector
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Versions of package lighter |
Release | Version | Architectures |
bookworm | 1.1.2-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.1.2-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.1.3-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.1.3-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
|
Lighter is a fast, memory-efficient tool for correcting sequencing
errors. Lighter avoids counting k-mers. Instead, it uses a pair of Bloom
filters, one holding a sample of the input k-mers and the other holding
k-mers likely to be correct. As long as the sampling fraction is
adjusted in inverse proportion to the depth of sequencing, Bloom filter
size can be held constant while maintaining near-constant accuracy.
Lighter is parallelized, uses no secondary storage, and is both faster
and more memory-efficient than competing approaches while achieving
comparable accuracy.
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loki
MCMC linkage analysis on general pedigrees
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Versions of package loki |
Release | Version | Architectures |
buster | 2.4.7.4-8 | amd64,arm64,armhf,i386 |
bullseye | 2.4.7.4-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 2.4.7.4-5 | amd64,armel,armhf,i386 |
bookworm | 2.4.7.4-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.4.7.4-12 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 2.4.7.4-12 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 2.4.7.4-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package loki: |
field | biology |
interface | commandline |
role | program |
scope | utility |
use | analysing |
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License: DFSG free
|
Performs Markov chain Monte Carlo multipoint linkage analysis on large,
complex pedigrees. The current package supports analyses on quantitative
traits only, although this restriction will be lifted in later versions.
Joint estimation of QTL number, position and effects uses Reversible Jump
MCMC. It is also possible to perform affected only IBD sharing analyses.
The package is enhanced by the following packages:
loki-doc
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ltrsift
postprocessing and classification of LTR retrotransposons
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Versions of package ltrsift |
Release | Version | Architectures |
buster | 1.0.2-8 | amd64,arm64,armhf,i386 |
sid | 1.0.2-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.0.2-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.0.2-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.0.2-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.0.2-7 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.0.2-1 | amd64,armel,armhf,i386 |
Debtags of package ltrsift: |
uitoolkit | gtk |
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License: DFSG free
|
LTRsift is a graphical desktop tool for semi-automatic postprocessing of de
novo predicted LTR retrotransposon annotations, such as the ones generated by
LTRharvest and LTRdigest. Its user-friendly interface displays LTR
retrotransposon candidates, their putative families and their internal
structure in a hierarchical fashion, allowing the user to "sift" through the
sometimes large results of de novo prediction software. It also offers
customizable filtering and classification functionality.
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lucy
DNA sequence quality and vector trimming tool
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Versions of package lucy |
Release | Version | Architectures |
trixie | 1.20-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.20-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.20-1 | amd64,arm64,armhf,i386 |
bullseye | 1.20-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.20-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
Lucy is a utility that prepares raw DNA sequence fragments for sequence
assembly, possibly using the TIGR Assembler. The cleanup process includes
quality assessment, confidence reassurance, vector trimming and vector
removal. The primary advantage of Lucy over other similar utilities is
that it is a fully integrated, stand alone program.
Lucy was designed and written at The Institute for Genomic Research
(TIGR, now the J. Craig Venter Institute), and it has been used here for
several years to clean sequence data from automated DNA sequencers prior
to sequence assembly and other downstream uses. The quality trimming
portion of lucy makes use of phred quality scores, such as those produced
by many automated sequencers based on the Sanger sequencing method. As
such, lucy’s quality trimming may not be appropriate for sequence
data produced by some of the new “next-generation” sequencers.
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lumpy-sv
general probabilistic framework for structural variant discovery
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Versions of package lumpy-sv |
Release | Version | Architectures |
bullseye | 0.3.1+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
trixie | 0.3.1+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
sid | 0.3.1+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
bookworm | 0.3.1+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
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License: DFSG free
|
LUMPY, a novel SV discovery framework that naturally integrates multiple
SV signals jointly across multiple samples. LUMPY yields improved
sensitivity, especially when SV signal is reduced owing to either low
coverage data or low intra-sample variant allele frequency.
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macs
Model-based Analysis of ChIP-Seq on short reads sequencers
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Versions of package macs |
Release | Version | Architectures |
buster | 2.1.2.1-1 | amd64,arm64,armhf,i386 |
trixie | 3.0.2-1 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
bookworm | 2.2.7.1-6 | amd64,arm64,armel,armhf,i386,ppc64el,s390x |
bullseye | 2.2.7.1-3 | amd64,arm64,armel,armhf,i386,ppc64el,s390x |
jessie | 2.0.9.1-1 | amd64,armel,armhf,i386 |
sid | 3.0.2-1 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
stretch | 2.1.1.20160309-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
MACS empirically models the length of the sequenced ChIP fragments, which
tends to be shorter than sonication or library construction size estimates,
and uses it to improve the spatial resolution of predicted binding sites.
MACS also uses a dynamic Poisson distribution to effectively capture local
biases in the genome sequence, allowing for more sensitive and robust
prediction. MACS compares favorably to existing ChIP-Seq peak-finding
algorithms, is publicly available open source, and can be used for ChIP-Seq
with or without control samples.
Please cite:
Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S. Johnson, Bradley E. Bernstein, Chad Nussbaum, Richard M. Myers, Myles Brown, Wei Li and X Shirley Liu:
Model-based Analysis of ChIP-Seq (MACS).
(PubMed,eprint)
Genome Biol.
9(9):R137
(2008)
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macsyfinder
detection of macromolecular systems in protein datasets
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Versions of package macsyfinder |
Release | Version | Architectures |
bullseye | 2.0~rc1-3 | amd64,i386 |
stretch | 1.0.2-3 | all |
bookworm | 2.0-2 | amd64,i386 |
trixie | 2.1.4-1 | amd64,arm64,i386 |
sid | 2.1.4-1 | amd64,arm64,i386 |
buster | 1.0.5-2 | all |
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License: DFSG free
|
MacSyFinder is a program to model and detect macromolecular systems,
genetic pathways... in protein datasets. In prokaryotes, these systems
have often evolutionarily conserved properties: they are made of conserved
components, and are encoded in compact loci (conserved genetic architecture).
The user models these systems with MacSyFinder to reflect these conserved
features, and to allow their efficient detection
This package presents the Open Source Java API to biological databases
and a series of mostly sequence-based algorithms.
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maffilter
process genome alignment in the Multiple Alignment Format
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Versions of package maffilter |
Release | Version | Architectures |
trixie | 1.3.1+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.3.1+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.1.0-1+dfsg-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.3.1+dfsg-1 | amd64,arm64,armhf,i386 |
bullseye | 1.3.1+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.3.1+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
MafFilter applies a series of "filters" to a MAF file, in order to
clean it, extract data and computer statistics while keeping track of
the associated meta-data such as genome coordinates and quality scores.
- It can process the alignment to remove low-quality / ambiguous /
masked regions.
- It can export data into a single or multiple alignment file in
format such as Fasta or Clustal.
- It can read annotation data in GFF or GTF format, and extract the
corresponding alignment.
- It can perform sliding windows calculations.
- It can reconstruct phylogeny/genealogy along the genome alignment.
- It can compute population genetics statistics, such as site
frequency spectrum, number of fixed/polymorphic sites, etc.
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mafft
Multiple alignment program for amino acid or nucleotide sequences
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Versions of package mafft |
Release | Version | Architectures |
bookworm | 7.505-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 7.407-2 | amd64,arm64,armhf,i386 |
jessie | 7.205-1 | amd64,armel,armhf,i386 |
stretch | 7.307-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 7.505-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 7.475-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 7.505-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package mafft: |
biology | format:aln, nuceleic-acids, peptidic |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | comparing |
works-with-format | plaintext |
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License: DFSG free
|
MAFFT is a multiple sequence alignment program which offers three
accuracy-oriented methods:
- L-INS-i (probably most accurate; recommended for <200 sequences;
iterative refinement method incorporating local pairwise alignment
information),
- G-INS-i (suitable for sequences of similar lengths; recommended for
<200 sequences; iterative refinement method incorporating global
pairwise alignment information),
-
E-INS-i (suitable for sequences containing large unalignable regions;
recommended for <200 sequences),
and five speed-oriented methods:
-
FFT-NS-i (iterative refinement method; two cycles only),
- FFT-NS-i (iterative refinement method; max. 1000 iterations),
- FFT-NS-2 (fast; progressive method),
- FFT-NS-1 (very fast; recommended for >2000 sequences; progressive
method with a rough guide tree),
- NW-NS-PartTree-1 (recommended for ∼50,000 sequences; progressive
method with the PartTree algorithm).
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malt
sequence alignment and analysis tool to process sequencing data
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Versions of package malt |
Release | Version | Architectures |
trixie | 0.5.2-3 | all |
sid | 0.5.2-3 | all |
bookworm | 0.5.2-2 | all |
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License: DFSG free
|
MALT, an acronym for MEGAN alignment tool, is a sequence alignment and
analysis tool designed for processing high-throughput sequencing data,
especially in the context of metagenomics. It is an extension of MEGAN6,
the MEGenome Analyzer and is designed to provide the input for MEGAN6,
but can also be used independently of MEGAN6.
The core of the program is a sequence alignment engine that aligns DNA
or protein sequences to a DNA or protein reference database in either
BLASTN (DNA queries and DNA references), BLASTX (DNA queries and protein
references) or BLASTP (protein queries and protein references) mode. The
engine uses a banded-alignment algorithm with ane gap scores and BLOSUM
substitution matrices (in the case of protein alignments). The program
can compute both local alignments (Smith-Waterman) or semi-global
alignments (in which reads are aligned end-to-end into reference
sequences), the latter being more appropriate for aligning metagenomic
reads to references.
The package is enhanced by the following packages:
multiqc
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mapdamage
tracking and quantifying damage patterns in ancient DNA sequences
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Versions of package mapdamage |
Release | Version | Architectures |
bookworm | 2.2.1+dfsg-3 | all |
trixie | 2.2.2+dfsg-1 | all |
buster | 2.0.9+dfsg-1 | all |
sid | 2.2.2+dfsg-1 | all |
bullseye | 2.2.1+dfsg-1 | all |
stretch | 2.0.6+dfsg-2 | all |
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License: DFSG free
|
MapDamage is a computational framework written in Python and R, which
tracks and quantifies DNA damage patterns among ancient DNA sequencing
reads generated by Next-Generation Sequencing platforms.
MapDamage is developed at the Centre for GeoGenetics by the
Orlando Group.
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mapsembler2
bioinformatics targeted assembly software
|
Versions of package mapsembler2 |
Release | Version | Architectures |
bookworm | 2.2.4+dfsg1-4 | amd64,arm64,ppc64el,s390x |
stretch | 2.2.3+dfsg-3 | amd64,arm64,armel,armhf,i386,ppc64el,s390x |
sid | 2.2.4+dfsg1-4 | amd64,arm64,ppc64el,s390x |
trixie | 2.2.4+dfsg1-4 | amd64,arm64,ppc64el,s390x |
jessie | 2.1.6+dfsg-1 | amd64,armel,armhf,i386 |
buster | 2.2.4+dfsg-3 | amd64,arm64,armhf,i386 |
bullseye | 2.2.4+dfsg1-3 | amd64,arm64,ppc64el,s390x |
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License: DFSG free
|
Mapsembler2 is a targeted assembly software.
It takes as input a set of NGS raw reads (fasta or fastq, gzipped or not)
and a set of input sequences (starters).
It first determines if each starter is read-coherent, e.g. whether reads
confirm the presence of each starter in the original sequence.
Then for each read-coherent starter, Mapsembler2 outputs its sequence
neighborhood as a linear sequence or as a graph, depending on the user choice.
Mapsembler2 may be used for (not limited to):
- Validate an assembled sequence (input as starter), e.g. from a de
Bruijn graph assembly where read-coherence was not enforced.
- Checks if a gene (input as starter) has an homolog in a set of reads
- Checks if a known enzyme is present in a metagenomic NGS read set.
- Enrich unmappable reads by extending them, possibly making them mappable
- Checks what happens at the extremities of a contig
- Remove contaminants or symbiont reads from a read set
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maq
maps short fixed-length polymorphic DNA sequence reads to reference sequences
|
Versions of package maq |
Release | Version | Architectures |
trixie | 0.7.1-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.7.1-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 0.7.1-7 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.7.1-8 | amd64,arm64,armhf,i386 |
jessie | 0.7.1-5 | amd64,armel,armhf,i386 |
bullseye | 0.7.1-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.7.1-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package maq: |
biology | nuceleic-acids |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing, comparing, searching |
works-with-format | plaintext |
|
License: DFSG free
|
Maq (short for Mapping and Assembly with Quality) builds mapping assemblies
from short reads generated by the next-generation sequencing machines. It was
particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has a
preliminary functionality to handle ABI SOLiD data. Maq is previously known as
mapass2.
Developmemt of Maq stopped in 2008. Its successors are BWA and SAMtools.
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maqview
graphical read alignment viewer for short gene sequences
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Versions of package maqview |
Release | Version | Architectures |
sid | 0.2.5-12 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 0.2.5-7 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.2.5-11 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.2.5-12 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.2.5-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 0.2.5-6 | amd64,armel,armhf,i386 |
buster | 0.2.5-9 | amd64,arm64,armhf,i386 |
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License: DFSG free
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Maqview is graphical read alignment viewer. It is specifically designed
for the Maq alignment file and allows you to see the mismatches, base
qualities and mapping qualities. Maqview is nothing fancy as Consed or
GAP, but just a simple viewer for you to see what happens in a
particular region.
In comparison to tgap-maq, the text-based read alignment viewer written
by James Bonfield, Maqview is faster and takes up much less memory and
disk space in indexing. This is possibly because tgap aims to be a
general-purpose viewer but Maqview fully makes use of the fact that a
Maq alignment file has already been sorted. Maqview is also efficient in
viewing and provides a command-line tool to quickly retrieve any region
in an Maq alignment file.
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mash
fast genome and metagenome distance estimation using MinHash
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Versions of package mash |
Release | Version | Architectures |
bookworm | 2.3+dfsg-3 | amd64,arm64,mips64el,ppc64el,s390x |
trixie | 2.3+dfsg-6 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
stretch | 1.1.1-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2.3+dfsg-6 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
buster | 2.1+dfsg-2 | amd64,arm64,armhf,i386 |
bullseye | 2.2.2+dfsg-2 | amd64,arm64,mips64el,ppc64el,s390x |
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License: DFSG free
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Mash uses MinHash locality-sensitive hashing to reduce large biosequences to
a representative sketch and rapidly estimate pairwise distances between
genomes or metagenomes. Mash sketch databases effectively delineate known
species boundaries, allow construction of approximate phylogenies, and can be
searched in seconds using assembled genomes or raw sequencing runs from
Illumina, Pacific Biosciences, and Oxford Nanopore.
For metagenomics, Mash scales to thousands of samples and can replicate Human
Microbiome Project and Global Ocean Survey results in a fraction of the time.
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massxpert
transitional package for massxpert -> massxpert2
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Versions of package massxpert |
Release | Version | Architectures |
sid | 8.5.0-2 | all |
jessie | 3.4.1-1 | amd64,armel,armhf,i386 |
bookworm | 7.0.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 6.0.2-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 3.6.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package massxpert: |
biology | nuceleic-acids, peptidic |
field | biology, chemistry |
interface | x11 |
role | program |
uitoolkit | qt |
use | analysing, simulating |
works-with | biological-sequence |
works-with-format | xml |
x11 | application |
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License: DFSG free
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This is a transitional package. It can safely be removed.
Runtime package.
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mauve-aligner
multiple genome alignment
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Versions of package mauve-aligner |
Release | Version | Architectures |
bookworm | 2.4.0+4736-6 | all |
buster | 2.4.0+4736-1 | amd64,arm64,armhf,i386 |
stretch | 2.4.0+4734-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2.4.0+4736-6 | all |
trixie | 2.4.0+4736-6 | all |
bullseye | 2.4.0+4736-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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Mauve is a system for efficiently constructing multiple genome alignments
in the presence of large-scale evolutionary events such as rearrangement
and inversion. Multiple genome alignment provides a basis for research
into comparative genomics and the study of evolutionary dynamics. Aligning
whole genomes is a fundamentally different problem than aligning short
sequences.
Mauve has been developed with the idea that a multiple genome aligner
should require only modest computational resources. It employs algorithmic
techniques that scale well in the amount of sequence being aligned. For
example, a pair of Y. pestis genomes can be aligned in under a minute,
while a group of 9 divergent Enterobacterial genomes can be aligned in
a few hours.
Mauve computes and interactively visualizes genome sequence comparisons.
Using FastA or GenBank sequence data, Mauve constructs multiple genome
alignments that identify large-scale rearrangement, gene gain, gene loss,
indels, and nucleotide substutition.
Mauve is developed at the University of Wisconsin.
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mcaller
find methylation in nanopore reads
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Versions of package mcaller |
Release | Version | Architectures |
sid | 1.0.3+git20210624.b415090-3 | all |
bookworm | 1.0.3+git20210624.b415090-3 | all |
trixie | 1.0.3+git20210624.b415090-3 | all |
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License: DFSG free
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H
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H-C-aller
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H
This program is designed to call m6A from nanopore data using the
differences between measured and expected currents.
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mecat2
ultra-fast and accurate de novo assembly tools for SMRT reads
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Versions of package mecat2 |
Release | Version | Architectures |
sid | 0.0+git20200428.f54c542+ds-4 | amd64 |
bullseye | 0.0+git20200428.f54c542+ds-3 | amd64 |
trixie | 0.0+git20200428.f54c542+ds-4 | amd64 |
bookworm | 0.0+git20200428.f54c542+ds-3 | amd64 |
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License: DFSG free
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An improved version of MECAT. It is an ultra-fast and accurate mapping
and error correcting de novo assembly tools for single molecula
sequencing (SMRT) reads. MECAT2 consists of the following three modules:
1. mecat2map: a fast and accurate alignment tool for SMRT reads.
2. mecat2cns: correct noisy reads based on their pairwise overlaps.
3. fsa: a string graph based assembly tool.
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megadepth
computes coverage from BigWig and BAM sequencing files
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Versions of package megadepth |
Release | Version | Architectures |
trixie | 1.2.0-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.2.0-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.2.0-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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A major concern for the interpretation of DNA and RNA (!) sequencing is
the number of reads that cover a particular area. This package
has interesting statistics for the distinction of coding and non-coding
parts of the genome and knows how to interpret transcripts that
span multiple exons.
This package is a successor of the program 'bamcount'.
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megahit
ultra-fast and memory-efficient meta-genome assembler
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Versions of package megahit |
Release | Version | Architectures |
sid | 1.2.9-5 | amd64 |
trixie | 1.2.9-5 | amd64 |
bookworm | 1.2.9-4 | amd64 |
bullseye | 1.2.9-2 | amd64 |
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License: DFSG free
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Megahit is an ultra-fast and memory-efficient NGS assembler. It is
optimized for metagenomes, but also works well on generic single genome
assembly (small or mammalian size) and single-cell assembly.
The software was praised in a Briefings in Bioinformatics 5/2020
review (DOI: 10.1093/bib/bbaa085).
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megan-ce
interactive tool to explore and analyse microbiome sequencing data
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Versions of package megan-ce |
Release | Version | Architectures |
sid | 6.21.1+dfsg-4 | all |
trixie | 6.21.1+dfsg-4 | all |
bookworm | 6.21.1+dfsg-2 | all |
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License: DFSG free
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MEGAN Community Edition is a shotgun sequencer to analyze microbiome samples.
It is a rewrite and extension of the widely-used microbiome analysis tool
MEGAN so as to facilitate the interactive analysis of the taxonomic and
functional content of very large microbiome datasets. Other new features
include a functional classifier called InterPro2GO, gene-centric read
assembly, principal coordinate analysis of taxonomy and function, and support
for metadata. By integrating MEGAN CE with the high-throughput DNA-to-protein
alignment tool DIAMOND a powerful and complete pipeline for the analysis of
metagenome shotgun sequences can be provided.
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melting
compute the melting temperature of nucleic acid duplex
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Versions of package melting |
Release | Version | Architectures |
stretch | 4.3.1+dfsg-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 5.2.0-2 | all |
bookworm | 5.2.0-2 | all |
sid | 5.2.0-2 | all |
bullseye | 5.2.0-2 | all |
buster | 5.2.0-1 | all |
jessie | 4.3.1+dfsg-1 | amd64,armel,armhf,i386 |
Debtags of package melting: |
biology | nuceleic-acids |
field | biology, biology:molecular |
interface | commandline |
role | program |
scope | utility |
suite | gnu |
use | analysing |
works-with-format | plaintext |
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License: DFSG free
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This program computes, for a nucleic acid duplex, the enthalpy, the
entropy and the melting temperature of the helix-coil
transitions. Three types of hybridisation are possible: DNA/DNA,
DNA/RNA, and RNA/RNA. The program first computes the hybridisation
enthalpy and entropy from the elementary parameters of each Crick's
pair by the nearest-neighbor method. Then the melting temperature is
computed. The set of thermodynamic parameters can be easily changed,
for instance following an experimental breakthrough.
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meryl
in- and out-of-core kmer counting and utilities
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Versions of package meryl |
Release | Version | Architectures |
sid | 0~20150903+r2013-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 0~20150903+r2013-6 | amd64,arm64,armhf,i386 |
bullseye | 0~20150903+r2013-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0~20150903+r2013-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0~20150903+r2013-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 0~20150903+r2013-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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meryl computes the kmer content of genomic sequences. Kmer
content is represented as a list of kmers and the number of
times each occurs in the input sequences. The kmer can be
restricted to only the forward kmer, only the reverse kmer,
or the canonical kmer (lexicographically smaller of the
forward and reverse kmer at each location). Meryl can
report the histogram of counts, the list of kmers and their
counts, or can perform mathematical and set operations
on the processed data files.
This package is part of the Kmer suite.
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metabat
robust statistical framework for reconstructing genomes from metagenomic data
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Versions of package metabat |
Release | Version | Architectures |
sid | 2.15-4 | amd64,i386 |
bookworm | 2.15-4 | amd64,i386 |
trixie | 2.15-4 | amd64,i386 |
bullseye | 2.15-3 | amd64,i386 |
upstream | 2.17 |
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License: DFSG free
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MetaBAT integrates empirical probabilistic distances of genome abundance
and tetranucleotide frequency for accurate metagenome binning. MetaBAT
outperforms alternative methods in accuracy and computational efficiency
on both synthetic and real metagenome datasets. It automatically forms
hundreds of high quality genome bins on a very large assembly consisting
millions of contigs in a matter of hours on a single node.
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metaeuk
sensitive, high-throughput gene discovery and annotation for metagenomics
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Versions of package metaeuk |
Release | Version | Architectures |
sid | 7-bba0d80+ds-1 | amd64,arm64,mips64el,ppc64el,riscv64 |
trixie | 7-bba0d80+ds-1 | amd64,arm64,mips64el,ppc64el,riscv64 |
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License: DFSG free
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MetaEuk is a modular toolkit designed for large-scale gene discovery and
annotation in eukaryotic metagenomic contigs. MetaEuk combines the fast and
sensitive homology search capabilities of MMseqs2 with a dynamic programming
procedure to recover optimal exons sets. It reduces redundancies in multiple
discoveries of the same gene and resolves conflicting gene predictions on the
same strand.
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metaphlan
Metagenomic Phylogenetic Analysis
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Versions of package metaphlan |
Release | Version | Architectures |
sid | 4.0.4-1 | all |
bookworm | 4.0.4-1 | all |
trixie | 4.0.4-1 | all |
upstream | 4.1.1 |
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License: DFSG free
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MetaPhlAn is a computational tool for profiling the composition of
microbial communities (Bacteria, Archaea and Eukaryotes) from
metagenomic shotgun sequencing data (i.e. not 16S) with species-level.
With the newly added StrainPhlAn module, it is now possible to perform
accurate strain-level microbial profiling.
MetaPhlAn relies on ~1.1M unique clade-specific marker genes (the latest
marker information file mpa_v31_CHOCOPhlAn_201901_marker_info.txt.bz2
can be found here) identified from ~100,000 reference genomes (~99,500
bacterial and archaeal and ~500 eukaryotic), allowing:
- unambiguous taxonomic assignments;
- accurate estimation of organismal relative abundance;
- species-level resolution for bacteria, archaea, eukaryotes and
viruses;
- strain identification and tracking
- orders of magnitude speedups compared to existing methods.
- metagenomic strain-level population genomics
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metastudent
predictor of Gene Ontology terms from protein sequence
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Versions of package metastudent |
Release | Version | Architectures |
bullseye | 2.0.1-8 | all |
jessie | 1.0.11-2 | all |
trixie | 2.0.1-10 | all |
bookworm | 2.0.1-9 | all |
sid | 2.0.1-10 | all |
stretch | 2.0.1-4 | all |
buster | 2.0.1-6 | all |
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License: DFSG free
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Often, only the sequence of a protein is known, but
not its functions. Metastudent will try to predict
missing functional annotations through homology searches (BLAST).
All predicted functions correspond to Gene Ontology (GO)
terms from the Molecular Function (MFO), the Biological Process
(BPO) and the Cellular Component Ontology (CCO) and are associated
with a reliability score.
Please cite:
Tobias Hamp, Rebecca Kassner, Stefan Seemayer, Esmeralda Vicedo, Christian Schaefer, Dominik Achten, Florian Auer, Ariane Boehm, Tatjana Braun, Maximilian Hecht, Mark Heron, Peter Hönigschmid, Thomas A. Hopf, Stefanie Kaufmann, Michael Kiening, Denis Krompass, Cedric Landerer, Yannick Mahlich, Manfred Roos and Burkhard Rost:
Homology-based inference sets the bar high for protein function prediction..
(PubMed)
BMC Bioinformatics
14(Suppl 3):S7
(2013)
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mhap
locality-sensitive hashing to detect long-read overlaps
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Versions of package mhap |
Release | Version | Architectures |
bookworm | 2.1.3+dfsg-3 | all |
stretch-backports | 2.1.3+dfsg-1~bpo9+1 | all |
stretch | 2.1.1+dfsg-1 | all |
trixie | 2.1.3+dfsg-3 | all |
sid | 2.1.3+dfsg-3 | all |
buster | 2.1.3+dfsg-2 | all |
bullseye | 2.1.3+dfsg-3 | all |
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License: DFSG free
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The MinHash Alignment Process (MHAP--pronounced MAP) is a
reference implementation of a probabilistic sequence overlapping
algorithm. Designed to efficiently detect all overlaps between noisy
long-read sequence data. It efficiently estimates Jaccard similarity
by compressing sequences to their representative fingerprints
composed on min-mers (minimum k-mer).
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microbegps
explorative taxonomic profiling tool for metagenomic data
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Versions of package microbegps |
Release | Version | Architectures |
bullseye | 1.0.0-5 | all |
sid | 1.0.0-7 | all |
stretch | 1.0.0-2 | all |
bookworm | 1.0.0-5 | all |
buster | 1.0.0-3 | all |
trixie | 1.0.0-7 | all |
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License: DFSG free
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MicrobeGPS is a bioinformatics tool for the analysis of metagenomic
sequencing data. The goal is to profile the composition of metagenomic
communities as accurately as possible and present the results to the
user in a convenient manner. One main focus is reliability: the tool
calculates quality metrics for the estimated candidates and allows the
user to identify false candidates easily.
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microbiomeutil
Microbiome Analysis Utilities
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Versions of package microbiomeutil |
Release | Version | Architectures |
bullseye | 20101212+dfsg1-4 | all |
sid | 20101212+dfsg1-6 | all |
trixie | 20101212+dfsg1-6 | all |
bookworm | 20101212+dfsg1-5 | all |
buster | 20101212+dfsg1-2 | all |
stretch | 20101212+dfsg1-1 | all |
jessie | 20101212+dfsg-1 | all |
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License: DFSG free
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The microbiomeutil package comes with the following utilities:
- ChimeraSlayer: ChimeraSlayer for chimera detection.
- NAST-iEr: NAST-based alignment tool.
- WigeoN: A reimplementation of the Pintail 16S anomaly
detection utility
- RESOURCES: Reference 16S sequences and NAST-alignments that
the tools above leverage.
Please cite:
Brian J. Haas, Dirk Gevers, Ashlee M. Earl, Mike Feldgarden, Doyle V. Ward, Georgia Giannoukos, Dawn Ciulla, Diana Tabbaa, Sarah K. Highlander, Erica Sodergren, Barbara Methé, Todd Z. DeSantis, The Human Microbiome Consortium, Joseph F. Petrosino, Rob Knight and Bruce W. Birren:
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.
(PubMed,eprint)
Genome Research
21(3):494-504
(2011)
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mindthegap
performs detection and assembly of DNA insertion variants in NGS read datasets
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Versions of package mindthegap |
Release | Version | Architectures |
bullseye | 2.2.2-2 | amd64,arm64,i386,mips64el,ppc64el,s390x |
sid | 2.3.0-4 | amd64,arm64,mips64el,ppc64el,riscv64 |
bookworm | 2.3.0-2 | amd64,arm64,mips64el,ppc64el |
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License: DFSG free
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Designed to call insertions of any size, whether they are novel or
duplicated, homozygous or heterozygous in the donor genome. It takes as
input a set of reads and a reference genome. It outputs two sets of
FASTA sequences: one is the set of breakpoints of detection insertion
sites, the other is the set of assembled insertions for each
breakpoint. MindTheGap can also be used as a genome assembly finishing
tool. It can fill the gaps between a set of input contigs without any a
priori on their relative order and orientation. It outputs the results
in gfa file.
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minexpert2
MS^n mass spectrometric data visualization and mining (runtime)
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Versions of package minexpert2 |
Release | Version | Architectures |
sid | 9.6.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 8.6.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 7.4.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 9.6.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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mineXpert2 allows the user to perform the following tasks:
- Open mass spectrometry data files (mzML, mzXML, asc, xy, ...);
- Display in a table view the full data set, for easy filtering;
- Calculate and display the TIC chromatogram;
- Calculate and display a mz=f(rt) color map;
- For mobility data, calculate and display a mz=f(dt) color map;
- Integrate the mass spectrometric data from any kind of data
representation (mass | drift spectra, TIC | XIC chromatogram,
2D color maps) to any other kind of data representation;
- For any mass data feature (mass peak, TIC | XIC peak, color map)
integrate to a XIC single intensity value;
- Powerful isotopic cluster calculation starting from a
chemical formula, optionally with user-defined isotopic abundance ratios;
- Gaussian fit over any isotopic cluster to estimate the
average mass of a given ion;
- Mouse-driven deconvolution of m/z data (charge envelope-based
or isotopic cluster-based);
- Export the data to text files;
- Export the graphical representation of mass spectrometric
data to graphics files in a number of formats (jpg, png, pdf).
This package ships the mineXpert2 program.
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minia
short-read biological sequence assembler
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Versions of package minia |
Release | Version | Architectures |
trixie | 3.2.6-4 | amd64,arm64,mips64el,ppc64el,riscv64 |
buster | 1.6906-2 | amd64,arm64,armhf,i386 |
stretch | 1.6906-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.6088-1 | amd64,armel,armhf,i386 |
bullseye | 3.2.1+git20200522.4960a99-1 | amd64,arm64,i386,mips64el,ppc64el,s390x |
bookworm | 3.2.6-3 | amd64,arm64,mips64el,ppc64el |
sid | 3.2.6-4 | amd64,arm64,mips64el,ppc64el,riscv64 |
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License: DFSG free
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What was referred to as "next-generation" DNA sequencing up to
the year 2020 delivered only "short" reads up to ~600 base pairs
in length that would then have to be puzzled by random overlaps
in their sequence towards a complete genome. This is the genome
assembly. And there are many biological pitfalls on long stretches
of low complexity regions and copy number variations and other
sorts of redundancies that render this difficult.
This package provides a short-read DNA sequence assembler based on a
de Bruijn graph, capable of assembling a human genome on a desktop
computer in a day.
The output of Minia is a set of contigs, i.e. stretches of gap-free
linear overlaps of short reads. In the best possible case this is
a whole chromosome.
Minia produces results of similar contiguity and accuracy to other
de Bruijn assemblers (e.g. Velvet).
Topics: Sequence assembly
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miniasm
ultrafast de novo assembler for long noisy DNA sequencing reads
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Versions of package miniasm |
Release | Version | Architectures |
bullseye | 0.3+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.3+dfsg-1 | amd64,arm64,armhf,i386 |
sid | 0.3+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 0.2+dfsg-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 0.3+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.3+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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Miniasm is an experimental very fast OLC-based de novo assembler for noisy
long reads. It takes all-vs-all read self-mappings (typically by minimap)
as input and outputs an assembly graph in the GFA format. Different from
mainstream assemblers, miniasm does not have a consensus step. It simply
concatenates pieces of read sequences to generate the final unitig sequences.
Thus the per-base error rate is similar to the raw input reads.
Topics: Sequence assembly
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minimac4
Fast Imputation Based on State Space Reduction HMM
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Versions of package minimac4 |
Release | Version | Architectures |
trixie | 4.1.6-1 | amd64 |
sid | 4.1.6-1 | amd64 |
buster | 1.0.0-2 | amd64 |
bookworm | 4.1.2-1 | amd64 |
bullseye | 1.0.2-2 | amd64 |
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License: DFSG free
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Minimac4 is a lower memory and more computationally efficient implementation
of "minimac2/3". It is an algorithm for genotypic imputation that works on
phased genotypes (say from MaCH).
Minimac4 is designed to handle very large reference panels in a more
computationally efficient way with no loss of accuracy. This algorithm
analyzes only the unique sets of haplotypes in small genomic segments, thereby
saving on time-complexity, computational memory but no loss in degree of
accuracy.
Please cite:
Sayantan Das, Lukas Forer, Sebastian Schönherr, Carlo Sidore, Adam E Locke, Alan Kwong, Scott I Vrieze, Emily Y Chew, Shawn Levy, Matt McGue, David Schlessinger, Dwight Stambolian, Po-Ru Loh, William G Iacono, Anand Swaroop, Laura J Scott, Francesco Cucca, Florian Kronenberg, Michael Boehnke, Gonçalo R Abecasis and Christian Fuchsberger:
Next-generation genotype imputation service and methods.
Nature Genetics
48(10):1284-1287
(2016)
|
|
minimap
tool for approximate mapping of long biosequences such as DNA reads
|
Versions of package minimap |
Release | Version | Architectures |
sid | 0.2-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.2-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 0.2-4 | amd64,arm64,armhf,i386 |
bullseye | 0.2-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.2-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 0.2-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
Minimap is an experimental tool to efficiently find multiple approximate
mapping positions between two sets of long biological sequences, such as
between DNA reads and reference genomes, between genomes and between long
noisy reads.
Minimap does not generate alignments as of now and because of this, it is
usually tens of times faster than mainstream aligners.
It does not replace mainstream aligners, but it can be useful when you
want to quickly identify long approximate matches at moderate divergence among
a huge collection of sequences. For this task, it is much faster than most
existing tools.
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minimap2
versatile pairwise aligner for genomic and spliced nucleotide sequences
|
Versions of package minimap2 |
Release | Version | Architectures |
bullseye | 2.17+dfsg-12 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch-backports | 2.15+dfsg-1~bpo9+1 | amd64,i386 |
bookworm | 2.24+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.27+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.27+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 2.15+dfsg-1 | amd64,i386 |
upstream | 2.28 |
|
License: DFSG free
|
Minimap2 is a versatile sequence alignment program that aligns DNA or
mRNA sequences against a large reference database. Typical use cases
include: (1) mapping PacBio or Oxford Nanopore genomic reads to the
human genome; (2) finding overlaps between long reads with error rate up
to ~15%; (3) splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA
or Direct RNA reads against a reference genome; (4) aligning Illumina
single- or paired-end reads; (5) assembly-to-assembly alignment; (6) full-
genome alignment between two closely related species with divergence
below ~15%.
For ~10kb noisy reads sequences, minimap2 is tens of times faster than
mainstream long-read mappers such as BLASR, BWA-MEM, NGMLR and GMAP. It
is more accurate on simulated long reads and produces biologically
meaningful alignment ready for downstream analyses. For >100bp Illumina
short reads, minimap2 is three times as fast as BWA-MEM and Bowtie2, and
as accurate on simulated data. Detailed evaluations are available from
the minimap2 paper or the preprint.
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mipe
Tools to store PCR-derived data
|
Versions of package mipe |
Release | Version | Architectures |
stretch | 1.1-5 | all |
bookworm | 1.1-9 | all |
trixie | 1.1-9 | all |
buster | 1.1-7 | all |
sid | 1.1-9 | all |
jessie | 1.1-4 | all |
bullseye | 1.1-9 | all |
Debtags of package mipe: |
field | biology, biology:bioinformatics, biology:molecular |
interface | commandline |
role | documentation, program |
scope | utility |
use | organizing |
works-with-format | xml |
|
License: DFSG free
|
MIPE provides a standard format to exchange and/or storage of all
information associated with PCR experiments using a flat text file. This will:
- allow for exchange of PCR data between researchers/laboratories
- enable traceability of the data
- prevent problems when submitting data to dbSTS or dbSNP
- enable the writing of standard scripts to extract data (e.g. a
list of PCR primers, SNP positions or haplotypes for different animals)
Although this tool can be used for data storage, it's primary focus
should be data exchange. For larger repositories, relational databases
are more appropriate for storage of these data. The MIPE format could
then be used as a standard format to import into and/or export from
these databases.
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mira-assembler
Whole Genome Shotgun and EST Sequence Assembler
|
Versions of package mira-assembler |
Release | Version | Architectures |
buster | 4.9.6-4 | amd64,arm64,armhf,i386 |
stretch | 4.9.6-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 4.9.6-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 4.9.6-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 4.9.6-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 4.9.6-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 4.0.2-1 | amd64,armel,armhf,i386 |
Debtags of package mira-assembler: |
role | program |
|
License: DFSG free
|
The mira genome fragment assembler is a specialised assembler for
sequencing projects classified as 'hard' due to high number of similar
repeats. For expressed sequence tags (ESTs) transcripts, miraEST is
specialised on reconstructing pristine mRNA transcripts while
detecting and classifying single nucleotide polymorphisms (SNP)
occurring in different variations thereof.
The assembler is routinely used for such various tasks as mutation
detection in different cell types, similarity analysis of transcripts
between organisms, and pristine assembly of sequences from various
sources for oligo design in clinical microarray experiments.
The package provides the following executables:
Binaries provided:
- mira: for assembly of genome sequences
- miramem: estimating memory needed to assemble projects.
- mirabait: a "grep" like tool to select reads with kmers up to 256 bases.
- miraconvert: is a tool to convert, extract and sometimes recalculate all
kinds of data related to sequence assembly files.
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|
mirtop
annotate miRNAs with a standard mirna/isomir naming
|
Versions of package mirtop |
Release | Version | Architectures |
bookworm | 0.4.25-2 | all |
bullseye | 0.4.23-2 | all |
sid | 0.4.28-2 | all |
trixie | 0.4.28-2 | all |
|
License: DFSG free
|
The main goal of this project is to create a reflection group on metazoan
microRNAs (miRNAs), open to all interested researchers, to identify blockages
and develop standards and guidelines to improve miRNA research, resources and
communication. This can go through the use of standardized file formats, gene
and variants nomenclature guidelines, and advancements in miRNA biology
understanding. The group will eventually also aim at expanding its breadth to
the development of novel tools, data resources, and best-practices guidelines
to benefit the scientific community by providing high confidence validated
research and analysis strategies, regardless the expertise in this field.
This package provides the command line interface to mirtop.
The package is enhanced by the following packages:
multiqc
Please cite:
Thomas Desvignes, Karen Eilbeck, Ioannis S. Vlachos, Bastian Fromm, Yin Lu, Marc K. Halushka, Michael Hackenberg, Gianvito Urgese, Elisa Ficarra, Shruthi Bandyadka, Jason Sydes, Peter Batzel, John H. Postlethwait, Phillipe Loher, Eric Londin, Aristeidis G. Telonis, Isidore Rigoutsos and Lorena Pantano Rubino:
miRTOP: An open source community project for the development of a unified format file for miRNA data [version 1; not peer reviewed].
(eprint)
F1000Research
7(ISCB Comm. J.):953 (Slides)
(2018)
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mlv-smile
Find statistically significant patterns in sequences
|
Versions of package mlv-smile |
Release | Version | Architectures |
bullseye | 1.47-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.47-6 | amd64,arm64,armhf,i386 |
stretch | 1.47-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.47-3 | amd64,armel,armhf,i386 |
sid | 1.47-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.47-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
Smile determines sequence motifs on the basis of a set of DNA, RNA or
protein sequences.
- No hard limit on the number of combinations of motifs to describe
subsets of sequences.
- The sequence alphabet may be specified.
- The use of wildcards is supported.
- Better determination of significance of motifs by simulation.
- Introduction of a set of sequences with negative controls
that should not match automatically determined motifs.
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|
mmb
model the structure and dynamics of macromolecules
|
Versions of package mmb |
Release | Version | Architectures |
trixie | 4.0.0+dfsg-5 | amd64,arm64,riscv64 |
experimental | 4.0.0+dfsg-3.1~exp1 | amd64,arm64,armhf |
bullseye | 3.2+dfsg-2+deb11u1 | amd64,arm64,ppc64el |
bookworm | 4.0.0+dfsg-2 | amd64,arm64 |
sid | 4.0.0+dfsg-5 | amd64,arm64,riscv64 |
|
License: DFSG free
|
MacroMoleculeBuilder, previously known as RNABuilder, can be used for morphing,
homology modeling, folding (e.g. using base pairing contacts), redesigning
complexes, fitting to low-resolution density maps, predicting local
rearrangements upon mutation, and many other applications.
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mmseqs2
ultra fast and sensitive protein search and clustering
|
Versions of package mmseqs2 |
Release | Version | Architectures |
trixie | 15-6f452+ds-2 | amd64,arm64,mips64el,ppc64el,riscv64 |
bookworm | 14-7e284+ds-1 | amd64,arm64,mips64el,ppc64el |
sid | 15-6f452+ds-2 | amd64,arm64,mips64el,ppc64el,riscv64 |
bullseye | 12-113e3+ds-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
upstream | 16-747c6 |
|
License: DFSG free
|
MMseqs2 (Many-against-Many sequence searching) is a software suite to
search and cluster huge proteins/nucleotide sequence sets. MMseqs2 is
open source GPL-licensed software implemented in C++ for Linux, MacOS,
and (as beta version, via cygwin) Windows. The software is designed to
run on multiple cores and servers and exhibits very good scalability.
MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it
achieves almost the same sensitivity. It can perform profile searches
with the same sensitivity as PSI-BLAST at over 400 times its speed.
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mosdepth
BAM/CRAM depth calculation biological sequencing
|
Versions of package mosdepth |
Release | Version | Architectures |
bullseye | 0.3.1+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
sid | 0.3.10+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
bookworm | 0.3.3+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
|
License: DFSG free
|
Many small reads are produced by high-throughput "next generation"
sequencing technologies. The final sequence is derived from how
these reads are overlapping towards a consensus.
The more reads are covering/confirming parts of a nucleotide seq,
the higher the confidence is. Too many reads would be indicative
of e.g. repeats in the genome.
mosdepth can output:
- per-base depth about 2x as fast samtools depth--about 25 minutes
of CPU time for a 30X genome.
- mean per-window depth given a window size--as would be used for
CNV calling.
- the mean per-region given a BED file of regions.
- a distribution of proportion of bases covered at or above a given
threshold for each chromosome and genome-wide.
- quantized output that merges adjacent bases as long as they fall
in the same coverage bins e.g. (10-20)
- threshold output to indicate how many bases in each region are
covered at the given thresholds.
when appropriate, the output files are bgzipped and indexed for ease
of use.
The package is enhanced by the following packages:
multiqc
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mothur
sequence analysis suite for research on microbiota
|
Versions of package mothur |
Release | Version | Architectures |
jessie | 1.33.3+dfsg-2 | amd64,armel,armhf,i386 |
sid | 1.48.1-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.44.3-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.41.21-1 | amd64,arm64,armhf,i386 |
stretch | 1.38.1.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 1.48.1-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.48.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 1.48.2 |
Debtags of package mothur: |
role | program |
|
License: DFSG free
|
Mothur seeks to develop a single piece of open-source, expandable
software to fill the bioinformatics needs of the microbial ecology
community. It has incorporated the functionality of dotur, sons,
treeclimber, s-libshuff, unifrac, and much more. In addition to improving
the flexibility of these algorithms, a number of other features including
calculators and visualization tools were added.
Please cite:
Patrick D Schloss, Sarah L Westcott, Thomas Ryabin, Justine R Hall, Martin Hartmann, Emily B Hollister, Ryan A Lesniewski, Brian B Oakley, Donovan H Parks, Courtney J Robinson, Jason W Sahl, Blaz Stres, Gerhard G Thallinger, David J Van Horn and Carolyn F Weber:
Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities.
(PubMed)
Appl Environ Microbiol
75(23):7537-7541
(2009)
Topics: Microbial ecology
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mptp
single-locus species delimitation
|
Versions of package mptp |
Release | Version | Architectures |
sid | 0.2.5-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 0.2.4-1 | amd64,arm64,armhf,i386 |
trixie | 0.2.5-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.2.4-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.2.4-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
Implementation of a fast species delimitation method, based on PTP
(Zhang et al. 2013) with a 64-bit multi-threaded design that handles
very large datasets.
The tool mPTP can handle very large biodiversity datasets. It implements
a fast method to compute the ML delimitation from an inferred
phylogenetic tree of the samples. Using MCMC, it also computes the
support values for each clade, which can be used to assess the
confidence of the ML delimitation.
ML delimitation mPTP implements two flavours of the point-estimate
solution. First, it implements the original method from (Zhang et al.
2013) where all within-species processes are modelled with a single
exponential distribution. mPTP uses a dynamic programming implementation
which estimates the ML delimitation faster and more accurately than the
original PTP. The dynamic programming implementation has similar
properties as (Gulek et al. 2010). See the wiki for more information.
The second method assumes a distinct exponential distribution for the
branching events of each of the delimited species allowing it to fit to
a wider range of empirical datasets.
MCMC method mPTP generates support values for each clades. They
represent the ratio of the number of samples for which a particular node
was in the between-species process, to the total number of samples.
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mrbayes
Bayesian Inference of Phylogeny
|
Versions of package mrbayes |
Release | Version | Architectures |
bookworm | 3.2.7a-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 3.2.7a-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 3.2.7a-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 3.2.7a-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 3.2.6+dfsg-2 | amd64,arm64,armhf,i386 |
stretch | 3.2.6+dfsg-1 | amd64,arm64,armhf,i386 |
jessie | 3.2.3+dfsg-1 | amd64,armel,armhf,i386 |
|
License: DFSG free
|
Bayesian inference of phylogeny is based upon a quantity called the posterior
probability distribution of trees, which is the probability of a tree
conditioned on the observations. The conditioning is accomplished using
Bayes's theorem. The posterior probability distribution of trees is
impossible to calculate analytically; instead, MrBayes uses a simulation
technique called Markov chain Monte Carlo (or MCMC) to approximate the
posterior probabilities of trees.
The package is enhanced by the following packages:
mrbayes-doc
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multiqc
output integration for RNA sequencing across tools and samples
|
Versions of package multiqc |
Release | Version | Architectures |
sid | 1.21+dfsg-2 | all |
bullseye | 1.9+dfsg-3 | all |
bookworm | 1.14+dfsg-1 | all |
trixie | 1.21+dfsg-2 | all |
upstream | 1.25.2 |
|
License: DFSG free
|
The sequencing of DNA or RNA with current high-throughput technologies
involves an array of tools and these are applied over a range of samples.
It is easy to loose oversight. And gathering the data and forwarding
them in a readable manner to the individuals who took the samples is
a challenge for a tool in itself. Well. Here it is.
MultiQC aggregates the output of multiple tools into a single report.
Reports are generated by scanning given directories for recognised log
files. These are parsed and a single HTML report is generated summarising
the statistics for all logs found. MultiQC reports can describe multiple
analysis steps and large numbers of samples within a single plot, and
multiple analysis tools making it ideal for routine fast quality control.
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mummer
Efficient sequence alignment of full genomes
|
Versions of package mummer |
Release | Version | Architectures |
sid | 3.23+dfsg-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 3.23~dfsg-2 | amd64,armel,armhf,i386 |
stretch | 3.23+dfsg-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 3.23+dfsg-4 | amd64,arm64,armhf,i386 |
bullseye | 3.23+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.23+dfsg-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 3.23+dfsg-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 4.0.0.~beta5 |
Debtags of package mummer: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | comparing |
works-with-format | plaintext |
|
License: DFSG free
|
MUMmer is a system for rapidly aligning entire genomes, whether
in complete or draft form. For example, MUMmer 3.0 can find all
20-basepair or longer exact matches between a pair of 5-megabase genomes
in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop
computer. MUMmer can also align incomplete genomes; it handles the 100s
or 1000s of contigs from a shotgun sequencing project with ease, and
will align them to another set of contigs or a genome using the NUCmer
program included with the system. If the species are too divergent for
DNA sequence alignment to detect similarity, then the PROmer program
can generate alignments based upon the six-frame translations of both
input sequences.
The package is enhanced by the following packages:
e-mem
Topics: Sequence analysis
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murasaki
homology detection tool across multiple large genomes
|
Versions of package murasaki |
Release | Version | Architectures |
bullseye | 1.68.6-12 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.68.6-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.68.6-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.68.6-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.68.6-8 | amd64,arm64,armhf,i386 |
bookworm | 1.68.6-13 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
Murasaki is a scalable and fast, language theory-based homology
detection tool across multiple large genomes. It enable whole-genome
scale multiple genome global alignments. Supports unlimited length
gapped-seed patterns and unique TF-IDF based filtering.
Murasaki is an anchor alignment software, which is
- exteremely fast (17 CPU hours for whole Human x Mouse genome (with
40 nodes: 52 wall minutes))
- scalable (Arbitrarily parallelizable across multiple nodes using MPI.
Even a single node with 16GB of ram can handle over 1Gbp of sequence.)
- unlimited pattern length
- repeat tolerant
- intelligent noise reduction
|
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murasaki-mpi
homology detection tool across multiple large genomes (MPI-version)
|
Versions of package murasaki-mpi |
Release | Version | Architectures |
trixie | 1.68.6-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.68.6-13 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.68.6-8 | amd64,arm64,armhf,i386 |
bullseye | 1.68.6-12 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.68.6-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.68.6-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
Murasaki is a scalable and fast, language theory-based homology
detection tool across multiple large genomes. It enable whole-genome
scale multiple genome global alignments. Supports unlimited length
gapped-seed patterns and unique TF-IDF based filtering.
Murasaki is an anchor alignment software, which is
- exteremely fast (17 CPU hours for whole Human x Mouse genome (with
40 nodes: 52 wall minutes))
- scalable (Arbitrarily parallelizable across multiple nodes using MPI.
Even a single node with 16GB of ram can handle over 1Gbp of sequence.)
- unlimited pattern length
- repeat tolerant
- intelligent noise reduction
This package provides the MPI-enabled binary for murasaki. While this
will speed up operation on multi-processor machines it will slow down
on a single processor.
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muscle
Multiple alignment program of protein sequences
|
Versions of package muscle |
Release | Version | Architectures |
bookworm | 5.1.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 5.1.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 5.1.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 3.8.31+dfsg-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 3.8.1551-2 | amd64,arm64,armhf,i386 |
bullseye | 3.8.1551-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 3.8.31-1 | amd64,armel,armhf,i386 |
upstream | 5.3 |
Debtags of package muscle: |
biology | format:aln, nuceleic-acids, peptidic |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | comparing |
works-with-format | plaintext |
|
License: DFSG free
|
MUSCLE is a multiple alignment program for protein sequences. MUSCLE
stands for multiple sequence comparison by log-expectation. In the
authors tests, MUSCLE achieved the highest scores of all tested
programs on several alignment accuracy benchmarks, and is also one of
the fastest programs out there.
Muscle v5 is a major re-write of MUSCLE based on new algorithms.
Users should be aware that command line arguments compared to version
3.x of MUSCLE have changed!
Highest accuracy, scalable to thousands of sequences
Compared to previous versions, Muscle v5 is much more accurate, is often
faster, and scales to much larger datasets. At the time of writing (late
2021), Muscle v5 has the highest scores on multiple alignment benchmarks
including Balibase, Bralibase, Prefab and Balifam. It can align tens of
thousands of sequences with high accuracy on a low-cost commodity computer
(say, an 8-core Intel CPU with 32 Gb RAM). On large datasets, Muscle v5
is 20-30% more accurate than MAFFT and Clustal-Omega.
Alignment ensembles
Muscle v5 can generate ensembles of high-accuracy alternative alignments.
All replicates have equal average accuracy on benchmark test, including
the MSA made with default parameters. By comparing results of downstream
analysis (trees, structure prediction...) on different replicates, you can
assess the effects of alignment errors on your study.
Topics: Sequence analysis
|
|
muscle3
multiple alignment program of protein sequences
|
Versions of package muscle3 |
Release | Version | Architectures |
sid | 3.8.1551-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 3.8.1551-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 3.8.1551-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
MUSCLE is a multiple alignment program for protein sequences. MUSCLE
stands for multiple sequence comparison by log-expectation. In the
authors tests, MUSCLE achieved the highest scores of all tested
programs on several alignment accuracy benchmarks, and is also one of
the fastest programs out there.
This is version 3 of the muscle program. It is a different program
than muscle version 5 which is packaged as muscle in Debian.
Topics: Sequence analysis
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|
mustang
multiple structural alignment of proteins
|
Versions of package mustang |
Release | Version | Architectures |
sid | 3.2.4-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 3.2.2-1 | amd64,armel,armhf,i386 |
stretch | 3.2.3-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 3.2.3-3 | amd64,arm64,armhf,i386 |
bullseye | 3.2.3-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.2.4-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 3.2.4-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package mustang: |
biology | peptidic |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
use | analysing, comparing |
works-with-format | plaintext |
|
License: DFSG free
|
Mustang is an algorithm to align multiple protein structures.
Given a set of PDB files, the program uses the spatial
information in the Calpha atoms of the set to produce a sequence alignment.
Based on a progressive pairwise heuristic the algorithm then proceeds
through a number of refinement passes. Mustang reports the multiple
sequence alignment and the corresponding superposition of structures.
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|
nanofilt
filtering and trimming of long read sequencing data
|
Versions of package nanofilt |
Release | Version | Architectures |
sid | 2.8.0-1 | all |
trixie | 2.8.0-1 | all |
bookworm | 2.8.0-1 | all |
bullseye | 2.6.0-3 | all |
|
License: DFSG free
|
Filtering and trimming of long read sequencing data. Filtering on
quality and/or read length, and optional trimming after passing filters.
Reads from stdin, writes to stdout. Optionally reads directly from an
uncompressed file specified on the command line.
Intended to be used:
1. directly after fastq extraction.
2. prior to mapping.
3. in a stream between extraction and mapping.
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|
nanolyse
remove lambda phage reads from a fastq file
|
Versions of package nanolyse |
Release | Version | Architectures |
bookworm | 1.2.0-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.2.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.2.0-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.2.0-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
NanoLyse is a tool for rapid removal of contaminant DNA, using the
Minimap2 aligner through the mappy Python binding. A typical application
would be the removal of the lambda phage control DNA fragment supplied
by ONT, for which the reference sequence is included in the package.
However, this approach may lead to unwanted loss of reads from regions
highly homologous to the lambda phage genome.
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|
nanook
pre- and post-alignment analysis of nanopore sequencing data
|
Versions of package nanook |
Release | Version | Architectures |
sid | 1.33+dfsg-6 | all |
trixie | 1.33+dfsg-6 | all |
bookworm | 1.33+dfsg-5 | all |
bullseye | 1.33+dfsg-2.1 | all |
buster | 1.33+dfsg-1 | all |
stretch-backports | 1.33+dfsg-1~bpo9+1 | all |
|
License: DFSG free
|
NanoOK is a flexible, multi-reference software for pre- and post-
alignment analysis of nanopore sequencing data, quality and error
profiles.
NanoOK (pronounced na-nook) is a tool for extraction, alignment and
analysis of Nanopore reads. NanoOK will extract reads as FASTA or FASTQ
files, align them (with a choice of alignment tools), then generate a
comprehensive multi-page PDF report containing yield, accuracy and
quality analysis. Along the way, it generates plain text files which can
be used for further analysis, as well as graphs suitable for inclusion
in presentations and papers.
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nanopolish
consensus caller for nanopore sequencing data
|
Versions of package nanopolish |
Release | Version | Architectures |
stretch | 0.5.0-1 | amd64,arm64,armel,i386,mips64el,mipsel,ppc64el |
stretch-backports | 0.10.2-1~bpo9+1 | amd64 |
buster | 0.11.0-2 | amd64 |
bookworm | 0.14.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
trixie | 0.14.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
bullseye | 0.13.2-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.14.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
|
License: DFSG free
|
Nanopolish uses a signal-level hidden Markov model for consensus calling
of nanopore genome sequencing data. It can perform signal-level analysis
of Oxford Nanopore sequencing data. Nanopolish can calculate an improved
consensus sequence for a draft genome assembly, detect base
modifications, call SNPs and indels with respect to a reference genome
and more.
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nanostat
statistics on long biological sequences
|
Versions of package nanostat |
Release | Version | Architectures |
sid | 1.4.0-3 | all |
bullseye | 1.4.0-3 | all |
bookworm | 1.4.0-3 | all |
|
License: DFSG free
|
NanoStat calculates various statistics from a long read sequencing
dataset in fastq, bam or albacore sequencing summary format.
It is meant to augment pipelines for the interpretation of
long DNA sequences as generated with the Nanopore.
This package provides the executable NanoStat.
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nanosv
structural variant caller for nanopore data
|
Versions of package nanosv |
Release | Version | Architectures |
trixie | 1.2.4+git20190409.c1ae30c-7 | all |
bookworm | 1.2.4+git20190409.c1ae30c-6 | all |
bullseye | 1.2.4+git20190409.c1ae30c-3 | all |
sid | 1.2.4+git20190409.c1ae30c-7 | all |
|
License: DFSG free
|
NanoSV is a software package that can be used to identify structural
genomic variations in long-read sequencing data, such as data produced
by Oxford Nanopore Technologies’ MinION, GridION or PromethION
instruments, or Pacific Biosciences RSII or Sequel sequencers. NanoSV
has been extensively tested using Oxford Nanopore MinION sequencing data.
Please cite:
Mircea Cretu Stancu, Markus J. van Roosmalen, Ivo Renkens, Marleen M. Nieboer, Sjors Middelkamp, Joep de Ligt, Giulia Pregno, Daniela Giachino, Giorgia Mandrile, Jose Espejo Valle-Inclan, Jerome Korzelius, Ewart de Bruijn, Edwin Cuppen, Michael E. Talkowski, Tobias Marschall, Jeroen de Ridder and Wigard P. Kloosterman:
Mapping and phasing of structural variation in patient genomes using nanopore sequencing..
(eprint)
Nature Communications
8:1326
(2017)
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nast-ier
NAST-based DNA alignment tool
|
Versions of package nast-ier |
Release | Version | Architectures |
sid | 20101212+dfsg1-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 20101212+dfsg1-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 20101212+dfsg1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 20101212+dfsg1-2 | amd64,arm64,armhf,i386 |
trixie | 20101212+dfsg1-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 20101212+dfsg1-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 20101212+dfsg-1 | amd64,armel,armhf,i386 |
|
License: DFSG free
|
The NAST-iEr alignment utility aligns a single raw nucleotide sequence
against one or more NAST formatted sequences.
The alignment algorithm involves global dynamic programming profile
alignment to fixed (NAST-formatted) multiply aligned template sequences
without any end-gap penalty.
NAST-iEr is part of the microbiomeutil suite.
Please cite:
Brian J. Haas, Dirk Gevers, Ashlee M. Earl, Mike Feldgarden, Doyle V. Ward, Georgia Giannoukos, Dawn Ciulla, Diana Tabbaa, Sarah K. Highlander, Erica Sodergren, Barbara Methé, Todd Z. DeSantis, The Human Microbiome Consortium, Joseph F. Petrosino, Rob Knight and Bruce W. Birren:
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.
(PubMed,eprint)
Genome Research
21(3):494-504
(2011)
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ncbi-acc-download
download genome files from NCBI by accession
|
Versions of package ncbi-acc-download |
Release | Version | Architectures |
sid | 0.2.8-3 | all |
bullseye | 0.2.7-1 | all |
trixie | 0.2.8-3 | all |
bookworm | 0.2.8-1 | all |
upstream | 0.2.9 |
|
License: DFSG free
|
This package provides a script to download sequences from GenBank/RefSeq
by accession through the NCBI ENTREZ API.
|
|
ncbi-blast+
next generation suite of BLAST sequence search tools
|
Versions of package ncbi-blast+ |
Release | Version | Architectures |
buster | 2.8.1-1+deb10u1 | amd64,arm64,armhf,i386 |
jessie | 2.2.29-3 | amd64,armel,armhf,i386 |
sid | 2.16.0+ds-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 2.16.0+ds-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.12.0+ds-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye-backports | 2.12.0+ds-3~bpo11+1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 2.6.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.11.0+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster-backports | 2.9.0-4~bpo10+1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch-backports-sloppy | 2.9.0-3~bpo9+1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package ncbi-blast+: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
use | analysing |
works-with | biological-sequence |
|
License: DFSG free
|
The Basic Local Alignment Search Tool (BLAST) is the most widely
used sequence similarity tool. There are versions of BLAST that
compare protein queries to protein databases, nucleotide queries
to nucleotide databases, as well as versions that translate nucleotide
queries or databases in all six frames and compare to protein databases
or queries.
PSI-BLAST produces a position-specific-scoring-matrix (PSSM) starting
with a protein query, and then uses that PSSM to perform further searches.
It is also possible to compare a protein or nucleotide query to a
database of PSSM’s.
The NCBI supports a BLAST web page at blast.ncbi.nlm.nih.gov as well as
a network service.
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|
ncbi-blast+-legacy
NCBI Blast legacy call script
|
Versions of package ncbi-blast+-legacy |
Release | Version | Architectures |
jessie | 2.2.29-3 | all |
buster | 2.8.1-1+deb10u1 | all |
stretch | 2.6.0-1 | all |
stretch-backports-sloppy | 2.9.0-3~bpo9+1 | all |
bookworm | 2.12.0+ds-3 | all |
buster-backports | 2.9.0-4~bpo10+1 | all |
bullseye | 2.11.0+ds-1 | all |
bullseye-backports | 2.12.0+ds-3~bpo11+1 | all |
trixie | 2.16.0+ds-6 | all |
sid | 2.16.0+ds-6 | all |
Debtags of package ncbi-blast+-legacy: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
|
License: DFSG free
|
This package adds some fake scripts to call NCBI+ programs
with the NCBI blast command line. It makes use of the
legacy_blast script in ncbi-blast+ package.
|
|
ncbi-entrez-direct
NCBI Entrez utilities on the command line
|
Versions of package ncbi-entrez-direct |
Release | Version | Architectures |
buster | 10.9.20190219+ds-1 | amd64,arm64,armhf,i386 |
trixie | 19.2.20230331+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 19.0.20230216+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 19.2.20230331+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 6.10.20170123+ds-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 14.6.20210224+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 23.2.20241219 |
|
License: DFSG free
|
Entrez Direct (EDirect) is an advanced method for accessing NCBI's set
of interconnected databases (publication, sequence, structure, gene,
variation, expression, etc.) from a terminal window or script.
Functions take search terms from command-line arguments. Individual
operations are combined to build multi-step queries. Record retrieval
and formatting normally complete the process.
EDirect also provides an argument-driven function that simplifies the
extraction of data from document summaries or other results that are
returned in structured XML format. This can eliminate the need for
writing custom software to answer ad hoc questions. Queries can move
seamlessly between EDirect commands and UNIX utilities or scripts to
perform actions that cannot be accomplished entirely within Entrez.
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ncbi-epcr
Tool to test a DNA sequence for the presence of sequence tagged sites
|
Versions of package ncbi-epcr |
Release | Version | Architectures |
jessie | 2.3.12-1-2 | amd64,armel,armhf,i386 |
buster | 2.3.12-1-7 | amd64,arm64,armhf,i386 |
bullseye | 2.3.12-1-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.3.12-1-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.3.12-1-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.3.12-1-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 2.3.12-1-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package ncbi-epcr: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | checking, searching |
works-with-format | plaintext |
|
License: DFSG free
|
Electronic PCR (e-PCR) is computational procedure that is used to identify
sequence tagged sites(STSs), within DNA sequences. e-PCR looks for potential
STSs in DNA sequences by searching for subsequences that closely match the
PCR primers and have the correct order, orientation, and spacing that could
represent the PCR primers used to generate known STSs.
The new version of e-PCR implements a fuzzy matching strategy. To reduce
likelihood that a true STS will be missed due to mismatches, multiple
discontiguous words may be used instead of a single exact word. Each of this
word has groups of significant positions separated by 'wildcard' positions
that are not required to match. In addition, it is also possible to allow
gaps in the primer alignments.
The main motivation for implementing reverse searching (called Reverse e-PCR)
was to make it feasible to search the human genome sequence and other large
genomes. The new version of e-PCR provides a search mode using a query
sequence against a sequence database.
This program is retired upstream and it is suggested to use Primer-Blast
https://www.ncbi.nlm.nih.gov/tools/primer-blast/
instead.
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ncbi-seg
tool to mask segments of low compositional complexity in amino acid sequences
|
Versions of package ncbi-seg |
Release | Version | Architectures |
sid | 0.0.20000620-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 0.0.20000620-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 0.0.20000620-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 0.0.20000620-5 | amd64,arm64,armhf,i386 |
bullseye | 0.0.20000620-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 0.0.20000620-2 | amd64,armel,armhf,i386 |
bookworm | 0.0.20000620-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
ncbi-seg (a.k.a. SEG) is a program for identifying and masking segments of
low compositional complexity in amino acid sequences.
ncbi-seg divides sequences into contrasting segments of low-complexity and
high-complexity. Low-complexity segments defined by the
algorithm represent "simple sequences" or "compositionally-biased regions".
This program is inappropriate for masking nucleotide sequences and, in fact,
may strip some nucleotide ambiguity codes from nt. sequences as they are being
read.
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ncbi-tools-bin
NCBI libraries for biology applications (text-based utilities)
|
Versions of package ncbi-tools-bin |
Release | Version | Architectures |
bullseye | 6.1.20170106+dfsg1-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 6.1.20170106+dfsg1-0+deb10u2 | amd64,arm64,armhf,i386 |
stretch | 6.1.20170106+dfsg1-0+deb9u1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 6.1.20120620-8 | amd64,armel,armhf,i386 |
sid | 6.1.20170106+dfsg2-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 6.1.20170106+dfsg2-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 6.1.20170106+dfsg1-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package ncbi-tools-bin: |
biology | nuceleic-acids, peptidic |
field | biology, biology:bioinformatics |
interface | commandline |
network | client |
role | program |
science | calculation |
scope | utility |
use | analysing, calculating, converting, searching |
works-with | biological-sequence |
works-with-format | plaintext, xml |
|
License: DFSG free
|
This package includes various utilities distributed with the NCBI C SDK,
including the development tools asntool and errhdr (formerly of
libncbi6-dev). None of the programs in this package require X; you can
find the X-based utilities in the ncbi-tools-x11 package. BLAST and
related tools now come from a separate source base, corresponding to the
ncbi-blast+ and ncbi-blast+-legacy packages.
The package is enhanced by the following packages:
mcl
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|
ncbi-tools-x11
NCBI libraries for biology applications (X-based utilities)
|
Versions of package ncbi-tools-x11 |
Release | Version | Architectures |
stretch | 6.1.20170106+dfsg1-0+deb9u1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 6.1.20170106+dfsg2-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 6.1.20170106+dfsg1-0+deb10u2 | amd64,arm64,armhf,i386 |
sid | 6.1.20170106+dfsg2-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 6.1.20170106+dfsg1-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 6.1.20120620-8 | amd64,armel,armhf,i386 |
bullseye | 6.1.20170106+dfsg1-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package ncbi-tools-x11: |
biology | nuceleic-acids, peptidic |
field | biology, biology:bioinformatics, biology:structural |
interface | 3d, x11 |
network | client |
role | program |
science | visualisation |
scope | utility |
uitoolkit | motif |
use | analysing, calculating, editing, searching, viewing |
x11 | application |
|
License: DFSG free
|
This package includes some X-based utilities distributed with the
NCBI C SDK: Network Entrez, Sequin, ddv, and udv. These programs
are not part of ncbi-tools-bin because they depend on several
additional library packages.
|
|
ncl-tools
tools to deal with NEXUS files
|
Versions of package ncl-tools |
Release | Version | Architectures |
bookworm | 2.1.21+git20210811.b1213a7-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.1.21+git20210811.b1213a7-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 2.1.21+git20190531.feceb81-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 2.1.18+dfsg-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2.1.21+git20210811.b1213a7-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 2.1.21+git20180827.c71b264-2 | amd64,arm64,armhf,i386 |
upstream | 2.1.21+git20231019.f845ec2 |
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License: DFSG free
|
The NEXUS Class Library is a C++ library for parsing NEXUS files.
The NEXUS file format is widely used in bioinformatics. Several popular
phylogenetic programs such as Paup, MrBayes, Mesquite, and MacClade use
this format.
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ncoils
coiled coil secondary structure prediction
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Versions of package ncoils |
Release | Version | Architectures |
trixie | 2002-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 2002-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2002-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 2002-4 | amd64,armel,armhf,i386 |
buster | 2002-7 | amd64,arm64,armhf,i386 |
bullseye | 2002-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2002-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
The program predicts the coiled coil secondary structure predictions
from protein sequences. The algorithm was published in
Lupas, van Dyke & Stock, Predicting coiled coils from
protein sequences Science, 252, 1162-1164, 1991.
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neobio
computes alignments of amino acid and nucleotide sequences
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Versions of package neobio |
Release | Version | Architectures |
sid | 0.0.20030929-6 | all |
jessie | 0.0.20030929-1.1 | all |
stretch | 0.0.20030929-2 | all |
buster | 0.0.20030929-4 | all |
bullseye | 0.0.20030929-6 | all |
bookworm | 0.0.20030929-6 | all |
trixie | 0.0.20030929-6 | all |
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License: DFSG free
|
Library and graphical user interface for pairwise sequence alignments.
Implementation of the dynamic programming methods of Needleman & Wunsch
(global alignment) and Smith & Waterman (local alignment).
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ngmlr
CoNvex Gap-cost alignMents for Long Reads
|
Versions of package ngmlr |
Release | Version | Architectures |
bookworm | 0.2.7+git20210816.a2a31fb+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.2.7+git20210816.a2a31fb+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.2.7+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
experimental | 0.2.7+git20210816.a2a31fb+dfsg-4~0exp0simde | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.2.7+git20210816.a2a31fb+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
|
Ngmlr is a long-read mapper designed to sensitively align PacBilo or
Oxford Nanopore to (large) reference genomes. It was designed to quickly
and correctly align the reads, including those spanning (complex)
structural variations. Ngmlr uses an SV aware k-mer search to find
approximate mapping locations for a read and then a banded Smith-
Waterman alignment algorithm to compute the final alignment. Ngmlr uses
a convex gap cost model that penalizes gap extensions for longer gaps
less than for shorter ones to compute precise alignments.
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njplot
phylogenetic tree drawing program
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Versions of package njplot |
Release | Version | Architectures |
jessie | 2.4-2 | amd64,armel,armhf,i386 |
sid | 2.4-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 2.4-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.4-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.4-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.4-8 | amd64,arm64,armhf,i386 |
stretch | 2.4-7 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package njplot: |
field | biology, biology:bioinformatics |
interface | x11 |
role | program |
scope | utility |
uitoolkit | motif |
use | analysing, editing, organizing, printing, viewing |
works-with | biological-sequence |
works-with-format | plaintext |
x11 | application |
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License: DFSG free
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NJplot is able to draw any dendrogram expressed in the Newick standard
phylogenetic tree format (e.g., the format used by the Phylip package).
NJplot is especially convenient for rooting the unrooted trees
obtained from parsimony, distance or maximum likelihood tree-building
methods.
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norsnet
tool to identify unstructured loops in proteins
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Versions of package norsnet |
Release | Version | Architectures |
bookworm | 1.0.17-7 | all |
bullseye | 1.0.17-6 | all |
jessie | 1.0.17-1 | all |
stretch | 1.0.17-2 | all |
trixie | 1.0.17-7 | all |
sid | 1.0.17-7 | all |
buster | 1.0.17-4 | all |
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License: DFSG free
|
NORSnet can distinguish between very long contiguous segments with
non-regular secondary structure (NORS regions) and well-folded proteins.
NORSnet was trained on predicted information rather than on experimental data.
This allows NORSnet to reach into regions in sequence space that are not
covered by specialized disorder predictors. One disadvantage of this approach
is that it is not optimal for the identification of the "average" disordered
region.
NORSnet takes the following input, further described on norsnet(1):
- a protein sequence in a FASTA file
- secondary structure and solvent accessibility prediction by prof(1)
- an HSSP file
- flexible/rigid residues prediction by profbval(1)
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norsp
predictor of non-regular secondary structure
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Versions of package norsp |
Release | Version | Architectures |
jessie | 1.0.6-1 | all |
bullseye | 1.0.6-6 | all |
bookworm | 1.0.6-7 | all |
trixie | 1.0.6-7 | all |
sid | 1.0.6-7 | all |
stretch | 1.0.6-2 | all |
buster | 1.0.6-4 | all |
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License: DFSG free
|
NORSp is a publicly available predictor for disordered regions in proteins.
Specifically, it predicts long regions with no regular secondary structure.
Upon submission of a protein sequence, NORSp analyses the protein about its
secondary structure, the presence of transmembrane helices and coiled-coils.
It then returns the presence and position of disordered regions.
NORSp can be useful for biologists in several ways. For example,
crystallographers can check whether their proteins contain NORS regions and
make the decision about whether to proceed with the experiments since NORS
proteins may be difficult to crystallise, as demonstrated by the their low
occurrence in PDB. Biologists interested in protein structure-function
relationship may also find it interesting to verify whether the
protein-protein interaction sites coincide with NORS regions.
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ntcard
Streaming algorithm to estimate cardinality in genomics datasets
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Versions of package ntcard |
Release | Version | Architectures |
bookworm | 1.2.2+dfsg-5 | amd64,arm64,mips64el,ppc64el |
sid | 1.2.2+dfsg-9 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
trixie | 1.2.2+dfsg-9 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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As input it takes file(s) in fasta, fastq, sam, or bam formats
and computes the total number of distinct k-mers, F0, and also
the k-mer coverage frequency histogram, fi, i>=1.
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nxtrim
Optimized trimming of Illumina mate pair reads
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Versions of package nxtrim |
Release | Version | Architectures |
bookworm | 0.4.3+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.4.3+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.4.3+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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This package helps rmove Nextera Mate Pair junction adapters
and categorise reads according to the orientation implied
by the adapter location.
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obitools
programs to analyze NGS data in a DNA metabarcoding context
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Versions of package obitools |
Release | Version | Architectures |
bullseye | 1.2.13+dfsg-3 | amd64 |
bookworm | 1.2.13+dfsg-5 | amd64 |
sid | 3.0.1~b26+dfsg-3 | amd64,arm64,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 3.0.1~b26+dfsg-3 | amd64,arm64,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.2.12+dfsg-2 | amd64 |
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License: DFSG free
|
The OBITools programs aims to help you to manipulate various data and
sequence files in a convenient way using the Unix command line interface.
They follow the standard Unix interface for command line program, allowing to
chain a set of commands using the pipe mechanism.
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openms
package for LC/MS data management and analysis
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Versions of package openms |
Release | Version | Architectures |
bookworm | 2.6.0+cleaned1-3 | all |
jessie | 1.11.1-5 | all |
bullseye | 2.6.0+cleaned1-3 | all |
sid | 2.6.0+cleaned1-4 | all |
trixie | 2.6.0+cleaned1-4 | all |
buster | 2.4.0-real-1 | all |
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License: DFSG free
|
OpenMS is a package for LC/MS data management and analysis. OpenMS
offers an infrastructure for the development of mass
spectrometry-related software and powerful 2D and 3D visualization
solutions.
TOPP (the OpenMS proteomic pipeline) is a pipeline for the analysis
of HPLC/MS data. It consists of a set of numerous small applications
that can be chained together to create analysis pipelines tailored
for a specific problem.
This package is a metapackage that depends on both the libopenms
library package (libOpenMS and libOpenMS_GUI) and the OpenMS
Proteomic Pipeline (topp) package.
Please cite:
Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert and Oliver Kohlbacher:
OpenMS – an Open-Source Software Framework for Mass Spectrometry.
(PubMed,eprint)
BMC Bioinformatics
9(163)
(2008)
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optimir
Integrating genetic variations in miRNA alignment
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Versions of package optimir |
Release | Version | Architectures |
trixie | 1.2-2 | all |
bookworm | 1.2-1 | all |
bullseye | 1.0-3 | all |
sid | 1.2-2 | all |
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License: DFSG free
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OptimiR is a miRSeq data alignment workflow. It integrates genetic information
to assess the impact of variants on miRNA expression.
OptimiR: A bioinformatics pipeline designed to detect and quantify miRNAs,
isomiRs and polymiRs from miRSeq data, & study the impact of genetic
variations on polymiRs' expression.
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pal2nal
converts proteins to genomic DNA alignment
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Versions of package pal2nal |
Release | Version | Architectures |
sid | 14.1-3 | all |
bullseye | 14.1-3 | all |
bookworm | 14.1-3 | all |
buster | 14.1-2 | all |
trixie | 14.1-3 | all |
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License: DFSG free
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PAL2NAL is a program that converts a multiple sequence alignment
of proteins and the corresponding DNA (or mRNA) sequences into
a codon-based DNA alignment. The program automatically assigns
the corresponding codon sequence even if the input DNA sequence
has mismatches with the input protein sequence, or contains UTRs,
polyA tails. It can also deal with frame shifts in the input
alignment, which is suitable for the analysis of pseudogenes.
The resulting codon-based DNA alignment can further be subjected
to the calculation of synonymous (Ks) and non-synonymous (Ka)
substitution rates.
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paleomix
pipelines and tools for the processing of ancient and modern HTS data
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Versions of package paleomix |
Release | Version | Architectures |
buster | 1.2.13.3-1 | amd64 |
trixie | 1.3.8-2 | amd64,arm64 |
sid | 1.3.8-2 | amd64,arm64 |
bullseye | 1.3.2-1 | amd64,arm64,mips64el,ppc64el |
bookworm | 1.3.7-3 | amd64,arm64 |
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License: DFSG free
|
The PALEOMIX pipelines are a set of pipelines and tools designed to aid
the rapid processing of High-Throughput Sequencing (HTS) data: The BAM
pipeline processes de-multiplexed reads from one or more samples,
through sequence processing and alignment, to generate BAM alignment
files useful in downstream analyses; the Phylogenetic pipeline carries
out genotyping and phylogenetic inference on BAM alignment files, either
produced using the BAM pipeline or generated elsewhere; and the Zonkey
pipeline carries out a suite of analyses on low coverage equine
alignments, in order to detect the presence of F1-hybrids in
archaeological assemblages. In addition, PALEOMIX aids in metagenomic
analysis of the extracts.
The pipelines have been designed with ancient DNA (aDNA) in mind, and
includes several features especially useful for the analyses of ancient
samples, but can all be for the processing of modern samples, in order
to ensure consistent data processing.
Please cite:
Mikkel Schubert, Luca Ermini, Clio Der Sarkissian, Hákon Jónsson, Aurélien Ginolhac, Robert Schaefer, Michael D Martin, Ruth Fernández, Martin Kircher, Molly McCue, Eske Willerslev and Ludovic Orlando:
Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX.
(PubMed)
Nature Protocols
9(5):1056-82
(2014)
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paml
Phylogenetic Analysis by Maximum Likelihood (PAML)
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Versions of package paml |
Release | Version | Architectures |
bookworm | 4.9j+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 4.9j+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 4.9j+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 4.8+dfsg-1 (non-free) | amd64 |
bullseye | 4.9j+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 4.8+dfsg-1 (non-free) | amd64 |
buster | 4.9h+dfsg-1 | amd64,arm64,armhf,i386 |
Debtags of package paml: |
role | program |
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License: DFSG free
|
PAML is a package of programs for phylogenetic analyses of DNA or
protein sequences using maximum likelihood. PAML is not good for tree
making. It may be used to estimate parameters and test hypotheses to
study the evolutionary process, when you have reconstructed trees using
other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc.
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paraclu
Parametric clustering of genomic and transcriptomic features
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Versions of package paraclu |
Release | Version | Architectures |
stretch | 9-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 9-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 9-2 | amd64,arm64,armhf,i386 |
bookworm | 10-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 10-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 9-1 | amd64,armel,armhf,i386 |
sid | 10-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
|
Paraclu finds clusters in data attached to sequences. It was first
applied to transcription start counts in genome sequences, but it
could be applied to other things too.
Paraclu is intended to explore the data, imposing minimal prior
assumptions, and letting the data speak for itself.
One consequence of this is that paraclu can find clusters within
clusters. Real data sometimes exhibits clustering at multiple scales:
there may be large, rarefied clusters; and within each large cluster
there may be several small, dense clusters.
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parasail
Aligner based on libparasail
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Versions of package parasail |
Release | Version | Architectures |
trixie | 2.6.2+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.6.2+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.6+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.4.3+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
This package contains a command-line aligner based on
libparasail. Parasail is a SIMD C library containing
implementations of the Smith-Waterman, Needleman-Wunsch,
and various semi-global pairwise sequence alignment algorithm.
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parsinsert
Parsimonious Insertion of unclassified sequences into phylogenetic trees
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Versions of package parsinsert |
Release | Version | Architectures |
trixie | 1.04-15 | amd64,arm64,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.04-15 | amd64,arm64,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.04-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.04-12 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.04-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.04-1 | amd64,armel,armhf,i386 |
buster | 1.04-4 | amd64,arm64,armhf,i386 |
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License: DFSG free
|
ParsInsert efficiently produces both a phylogenetic tree and taxonomic
classification for sequences for microbial community sequence analysis. This
is a C++ implementation of the Parsimonious Insertion algorithm.
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parsnp
rapid core genome multi-alignment
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Versions of package parsnp |
Release | Version | Architectures |
trixie | 2.0.6+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.2+dfsg-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.2+dfsg-5 | amd64,arm64,armhf,i386 |
sid | 2.0.6+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.5.4+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.7.4+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 2.1.2 |
|
License: DFSG free
|
Parsnp was designed to align the core genome of hundreds to thousands of
bacterial genomes within a few minutes to few hours. Input can be both
draft assemblies and finished genomes, and output includes variant (SNP)
calls, core genome phylogeny and multi-alignments. Parsnp leverages
contextual information provided by multi-alignments surrounding SNP
sites for filtration/cleaning, in addition to existing tools for
recombination detection/filtration and phylogenetic reconstruction.
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patman
rapid alignment of short sequences to large databases
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Versions of package patman |
Release | Version | Architectures |
bullseye | 1.2.2+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.2.2+dfsg-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.2.2+dfsg-5 | amd64,arm64,armhf,i386 |
trixie | 1.2.2+dfsg-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.2.2+dfsg-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
Patman searches for short patterns in large DNA databases, allowing
for approximate matches. It is optimized for searching for many small
pattern at the same time, for example microarray probes.
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pbdagcon
sequence consensus using directed acyclic graphs
|
Versions of package pbdagcon |
Release | Version | Architectures |
stretch | 0.3+20161121+ds-1 | amd64,arm64,mips64el,ppc64el |
trixie | 0.3+git20180411.c14c422+dfsg-9 | amd64,arm64,mips64el,ppc64el,riscv64 |
buster | 0.3+git20161121.0000000+ds-1.1 | amd64,arm64 |
bullseye | 0.3+git20180411.c14c422+dfsg-1 | amd64,arm64,mips64el,ppc64el |
bookworm | 0.3+git20180411.c14c422+dfsg-8 | amd64,arm64,mips64el,ppc64el |
sid | 0.3+git20180411.c14c422+dfsg-9 | amd64,arm64,mips64el,ppc64el,riscv64 |
|
License: DFSG free
|
pbdagcon is a tool that implements DAGCon (Directed Acyclic Graph Consensus)
which is a sequence consensus algorithm based on using directed acyclic
graphs to encode multiple sequence alignment.
It uses the alignment information from blasr to align sequence reads to a
"backbone" sequence. Based on the underlying alignment directed acyclic graph
(DAG), it will be able to use the new information from the reads to find the
discrepancies between the reads and the "backbone" sequences. A dynamic
programming process is then applied to the DAG to find the optimum sequence
of bases as the consensus. The new consensus can be used as a new backbone
sequence to iteratively improve the consensus quality.
While the code is developed for processing PacBio(TM) raw sequence data,
the algorithm can be used for general consensus purpose. Currently, it only
takes FASTA input. For shorter read sequences, one might need to adjust the
blasr alignment parameters to get the alignment string properly.
The code and the underlying graphical data structure have been used for some
algorithm development prototyping including phasing reads and pre-assembly.
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pbhoney
genomic structural variation discovery
|
Versions of package pbhoney |
Release | Version | Architectures |
sid | 15.8.24+dfsg-8 | all |
bookworm | 15.8.24+dfsg-7 | all |
trixie | 15.8.24+dfsg-8 | all |
buster | 15.8.24+dfsg-3 | all |
stretch | 15.8.24+dfsg-2 | all |
bullseye | 15.8.24+dfsg-7 | all |
|
License: DFSG free
|
PBHoney is an implementation of two variant-identification
approaches designed to exploit the high mappability of long reads
(i.e., greater than 10,000 bp). PBHoney considers both intra-read
discordance and soft-clipped tails of long reads to identify
structural variants.
PBHoney is part of the PBSuite.
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pbjelly
genome assembly upgrading tool
|
Versions of package pbjelly |
Release | Version | Architectures |
bookworm | 15.8.24+dfsg-7 | all |
sid | 15.8.24+dfsg-8 | all |
trixie | 15.8.24+dfsg-8 | all |
bullseye | 15.8.24+dfsg-7 | all |
buster | 15.8.24+dfsg-3 | all |
stretch | 15.8.24+dfsg-2 | all |
|
License: DFSG free
|
PBJelly is a highly automated pipeline that aligns long sequencing
reads (such as PacBio RS reads or long 454 reads in fasta format)
to high-confidence draft assembles. PBJelly fills or reduces as
many captured gaps as possible to produce upgraded draft genomes.
PBJelly is part of the PBSuite.
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pbsim
simulator for PacBio sequencing reads
|
Versions of package pbsim |
Release | Version | Architectures |
sid | 1.0.3+git20180330.e014b1d+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.0.3+git20180330.e014b1d+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.0.3+git20180330.e014b1d+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.3+git20180330.e014b1d+dfsg-1 | amd64,arm64,armhf,i386 |
trixie | 1.0.3+git20180330.e014b1d+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.0.3-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
PacBio DNA sequencers produce two types of characteristic reads: CCS
(short and low error rate) and CLR (long and high error rate), both of
which could be useful for de novo assembly of genomes. PBSIM simulates
those PacBio reads from a reference sequence by using either a model-based
or sampling-based simulation. Simulated reads are useful, for example, when
developing or evaluating sequence assemblers targeted at PacBio data.
Topics: Sequence analysis
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pbsuite
software for Pacific Biosciences sequencing data
|
Versions of package pbsuite |
Release | Version | Architectures |
bullseye | 15.8.24+dfsg-7 | all |
buster | 15.8.24+dfsg-3 | all |
bookworm | 15.8.24+dfsg-7 | all |
trixie | 15.8.24+dfsg-8 | all |
stretch | 15.8.24+dfsg-2 | all |
sid | 15.8.24+dfsg-8 | all |
|
License: DFSG free
|
The PBSuite contains two projects created for analysis of
Pacific Biosciences long-read sequencing data.
- PBJelly - genome upgrading tool
- PBHoney - structural variation discovery
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pdb2pqr
Preparation of protein structures for electrostatics calculations
|
Versions of package pdb2pqr |
Release | Version | Architectures |
bookworm | 3.5.2+dfsg-3 | all |
sid | 3.6.1+dfsg-1 | all |
trixie | 3.6.1+dfsg-1 | all |
jessie | 1.9.0+dfsg-1 | amd64,armel,armhf,i386 |
stretch | 2.1.1+dfsg-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.1.1+dfsg-5 | amd64,arm64,armhf,i386 |
bullseye | 2.1.1+dfsg-7+deb11u1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 3.6.2 |
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License: DFSG free
|
PDB2PQR is a Python software package that automates many of the common
tasks of preparing structures for continuum electrostatics calculations.
It thus provides a platform-independent utility for converting protein files
in PDB format to PQR format. These tasks include:
- Adding a limited number of missing heavy atoms to biomolecular structures
- Determining side-chain pKas
- Placing missing hydrogens
- Optimizing the protein for favorable hydrogen bonding
- Assigning charge and radius parameters from a variety of force fields
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perlprimer
Graphical design of primers for PCR
|
Versions of package perlprimer |
Release | Version | Architectures |
sid | 1.2.4-2 | all |
bullseye | 1.2.4-2 | all |
bookworm | 1.2.4-2 | all |
trixie | 1.2.4-2 | all |
stretch | 1.2.3-1 | all |
jessie | 1.1.21-2 | all |
buster | 1.2.4-1 | all |
Debtags of package perlprimer: |
biology | format:aln, nuceleic-acids, peptidic |
field | biology, biology:molecular |
interface | x11 |
network | client |
role | program |
scope | utility |
uitoolkit | tk |
use | analysing |
works-with-format | plaintext |
x11 | application |
|
License: DFSG free
|
PerlPrimer is a free, open-source GUI application written in Perl that designs
primers for standard Polymerase Chain Reaction (PCR), bisulphite PCR,
real-time PCR (QPCR) and sequencing. It aims to automate and simplify the
process of primer design.
If operated online, the tool nicely communicates with the Ensembl
project for further insights into the gene structure, i.e., allowing
for taking the location of exons and introns into account for the design
of the primers. The sequences themselves can be retrieved, too.
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perm
efficient mapping of short reads with periodic spaced seeds
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Versions of package perm |
Release | Version | Architectures |
stretch | 0.4.0-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0.4.0-1 | amd64,armel,armhf,i386 |
trixie | 0.4.0-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 0.4.0-4 | amd64,arm64,armhf,i386 |
sid | 0.4.0-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.4.0-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.4.0-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
PerM is a software package which was designed to perform highly efficient
genome scale alignments for hundreds of millions of short reads produced by
the ABI SOLiD and Illumina sequencing platforms. Today PerM is capable of
providing full sensitivity for alignments within 4 mismatches for 50bp SOLID
reads and 9 mismatches for 100bp Illumina reads.
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pftools
build and search protein and DNA generalized profiles
|
Versions of package pftools |
Release | Version | Architectures |
bullseye | 3.2.6-1 | amd64 |
buster | 3+dfsg-3 | amd64 |
stretch-backports | 3+dfsg-3~bpo9+1 | amd64 |
sid | 3.2.12-1 | amd64 |
trixie | 3.2.12-1 | amd64 |
bookworm | 3.2.12-1 | amd64 |
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License: DFSG free
|
The pftools package contains all the software necessary to build protein
and DNA generalized profiles and use them to scan and align sequences,
and search databases.
File formats used by the pftools
- Generalized profiles format and syntax.
- The multiple sequence alignment format (PSA).
- The extended header multiple sequence alignment format (XPSA).
Programs to build generalized profiles
pfmake
Build a profile from a multiple sequence alignment.
pfscale
Fit parameters of an extreme-value distribution to a profile score list.
pfw
Weight sequences of a multiple sequence alignment to correct for
sampling bias.
Programs to search with generalized profiles
pfsearch / pfsearchV3
Search a protein or DNA sequence library for sequence segments matching
a profile (V3 is the new version of this tool).
pfscan
Scan a protein or DNA sequence with a profile library
Conversion programs
psa2msa
Reformat PSA file to Pearson/Fasta multiple sequence alignment file.
ptof
Convert a protein profile into a frame-search profile to search DNA
sequences. To be used with 2ft.
2ft
Converts both strands of DNA into so-called interleaved
frame-translated DNA sequences to search with protein profiles. To be
used with ptof.
6ft
Translates all six reading frames of a double-stranded DNA sequence
into individual protein sequences.
pfgtop
Convert a profile in GCG format into PROSITE format.
pfhtop
Convert a HMMER1 ASCII-formatted HMM into an equivalent PROSITE profile.
ptoh
Converts a generalized profile into an approximately equivalent HMM
profile in HMMER1 format (can be read by the hmmconvert program from
the HMMER2 package).
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phast
phylogenetic analysis with space/time models
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Versions of package phast |
Release | Version | Architectures |
sid | 1.7+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.5+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.4+dfsg-1 | amd64,arm64,armhf,i386 |
bookworm | 1.6+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.7+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
PHAST is a software package for comparative and evolutionary genomics.
It consists of about half a dozen major programs, plus more than a dozen
utilities for manipulating sequence alignments, phylogenetic trees, and
genomic annotations. For the most part, PHAST focuses on two kinds of
applications: the identification of novel functional elements, including
protein-coding exons and evolutionarily conserved sequences; and
statistical phylogenetic modeling, including estimation of model
parameters, detection of signatures of selection, and reconstruction of
ancestral sequences.
PHAST does not support phylogeny reconstruction or sequence alignment,
and it is designed for use with DNA sequences only (see Comparison).
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phipack
PHI test and other tests of recombination
|
Versions of package phipack |
Release | Version | Architectures |
bookworm | 0.0.20160614-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.0.20160614-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.0.20160614-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 0.0.20160614-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.0.20160614-3 | amd64,arm64,armhf,i386 |
bullseye | 0.0.20160614-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
The PhiPack software package implements a few tests for recombination
and can produce refined incompatibility matrices as well. Specifically,
PHIPack implements the 'Pairwise Homoplasy Index', Maximum Chi2 and the
'Neighbour Similarity Score'. The program Phi can be run to produce a
p-value of recombination within a data set and the program profile can
be run to determine regions exhibiting strongest evidence mosaicism.
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phybin
binning/clustering newick trees by topology
|
Versions of package phybin |
Release | Version | Architectures |
trixie | 0.3-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.3-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.3-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 0.3-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x |
buster | 0.3-3 | amd64,arm64,armhf,i386 |
bookworm | 0.3-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
PhyBin is a simple command line tool that classifies a set of Newick
tree files by their topology. The purpose of it is to take a large set
of tree files and browse through the most common tree topologies.
It can do simple binning of identical trees or more complex clustering
based on an all-to-all Robinson-Foulds distance matrix.
phybin produces output files that characterize the size and contents of
each bin or cluster (including generating GraphViz-based visual
representations of the tree topologies).
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phylip
package of programs for inferring phylogenies
|
Versions of package phylip |
Release | Version | Architectures |
jessie | 3.696+dfsg-1 | amd64,armel,armhf,i386 |
sid | 3.697+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 3.697+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 3.697+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 3.697+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 3.697+dfsg-1 | amd64,arm64,armhf,i386 |
stretch | 3.696+dfsg-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package phylip: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing, comparing |
works-with-format | plaintext |
|
License: DFSG free
|
The PHYLogeny Inference Package is a package of programs for inferring
phylogenies (evolutionary trees) from sequences.
Methods that are available in the package include parsimony, distance
matrix, and likelihood methods, including bootstrapping and consensus
trees. Data types that can be handled include molecular sequences, gene
frequencies, restriction sites, distance matrices, and 0/1 discrete
characters.
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phylonium
Fast and Accurate Estimation of Evolutionary Distances
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Versions of package phylonium |
Release | Version | Architectures |
trixie | 1.7-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.6-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.7-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
|
This is the phylonium program for estimating the evolutionary distances
between closely related genomes. It is much faster than alignment based
approaches for phylogeny reconstruction and usually more accurate than
competing alignment-free methods.
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phyml
Phylogenetic estimation using Maximum Likelihood
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Versions of package phyml |
Release | Version | Architectures |
trixie | 3.3.20220408-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 20120412-2 | amd64,armel,armhf,i386 |
bookworm | 3.3.20220408-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 3.3.20220408-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 3.3.20180621-2 | amd64,arm64,armhf,i386 |
stretch | 3.2.0+dfsg-7 | amd64,arm64,armhf,i386 |
bullseye | 3.3.20200621-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package phyml: |
biology | peptidic |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
use | analysing, comparing |
works-with | biological-sequence |
|
License: DFSG free
|
PhyML is a software that estimates maximum likelihood phylogenies from
alignments of nucleotide or amino acid sequences. It provides a wide
range of options that were designed to facilitate standard phylogenetic
analyses. The main strengths of PhyML lies in the large number of
substitution models coupled to various options to search the space of
phylogenetic tree topologies, going from very fast and efficient methods
to slower but generally more accurate approaches. It also implements
two methods to evaluate branch supports in a sound statistical framework
(the non-parametric bootstrap and the approximate likelihood ratio test).
PhyML was designed to process moderate to large data sets. In theory,
alignments with up to 4,000 sequences 2,000,000 character-long can
be analyzed. In practice however, the amount of memory required to process
a data set is proportional of the product of the number of sequences by their
length. Hence, a large number of sequences can only be processed provided
that they are short. Also, PhyML can handle long sequences provided that
they are not numerous. With most standard personal computers, the “comfort
zone” for PhyML generally lies around 3 to 500 sequences less than 2,000
character long.
This package also includes PhyTime.
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physamp
sample sequence alignment corresponding to phylogeny
|
Versions of package physamp |
Release | Version | Architectures |
stretch | 0.2.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.1.0-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.1.0-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.1.0-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.1.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.1.0-1 | amd64,arm64,armhf,i386 |
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License: DFSG free
|
The PhySamp package currently contains two programs: bppphysamp, which
samples sequences according to their similarity, and bppalnoptim, which
samples a sequence alignment by removing sequences in order to maximize
the number of sites suitable for a given analysis. The bppalnoptim
program has three running modes:
- Interactive: the user will be iteratively proposed a set of choices
for sequence removal, with their corresponding site gains. The
procedure stops when the user does not want to remove more sequences,
and the resulting filtered alignment is written.
- Automatic: the user enters an a priori criterion for stopping
the filtering procedure (for instance a minimum number of
sequences to keep).
- Diagnostic: this mode allows one to plot the trade-off curve, by
showing the site gain as a function of the number of removed
sequences.
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phyutility
simple analyses or modifications on both phylogenetic trees and data matrices
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Versions of package phyutility |
Release | Version | Architectures |
bullseye | 2.7.3+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.7.3+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 2.7.3-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.7.3-1 | amd64,armel,armhf,i386 |
sid | 2.7.3+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.7.3+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.7.3+dfsg-2 | amd64,arm64,armhf,i386 |
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License: DFSG free
|
Phyutility (fyoo-til-i-te) is a command line program that performs
simple analyses or modifications on both trees and data matrices.
Currently it performs the following functions (to suggest another
feature, submit an Issue and use the label Type-Enhancement) :
Trees
- rerooting
- pruning
- type conversion
- consensus
- leaf stability
- lineage movement
- tree support
Data Matrices
- concatenate alignments
- genbank parsing
- trimming alignments
- search NCBI
- fetch NCBI
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phyx
UNIX-style phylogenetic analyses on trees and sequences
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Versions of package phyx |
Release | Version | Architectures |
bullseye | 1.01+ds-2+deb11u1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.3+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.999+ds-1 | amd64,arm64,armhf,i386 |
trixie | 1.3.2+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.3.2+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
phyx provides a convenient, lightweight and inclusive toolkit consisting of
programs spanning the wide breadth of programs utilized by researchers
performing phylogenomic analyses. Modeled after Unix/GNU/Linux command
line tools, individual programs perform a single task and operate on
standard I/O streams. A result of this stream-centric approach is that, for
most programs, only a single sequence or tree is in memory at any moment.
Thus, large datasets can be processed with minimal memory requirements.
phyx’s ever-growing complement of programs consists of over 35 programs
focused on exploring, manipulating, analyzing and simulating phylogenetic
objects (alignments, trees and MCMC logs). As with standard Unix command
line tools, these programs can be piped (together with non-phyx tools),
allowing the easy construction of efficient analytical pipelines.
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picard-tools
Command line tools to manipulate SAM and BAM files
|
Versions of package picard-tools |
Release | Version | Architectures |
bullseye | 2.24.1+dfsg-1 | all |
buster | 2.18.25+dfsg-2 | amd64 |
jessie | 1.113-1 | all |
stretch | 2.8.1+dfsg-1 | all |
trixie | 3.1.1+dfsg-1 | all |
bookworm | 2.27.5+dfsg-2 | all |
sid | 3.1.1+dfsg-1 | all |
upstream | 3.3.0 |
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License: DFSG free
|
SAM (Sequence Alignment/Map) format is a generic format for storing
large nucleotide sequence alignments. Picard Tools includes these
utilities to manipulate SAM and BAM files:
AddCommentsToBam FifoBuffer
AddOrReplaceReadGroups FilterSamReads
BaitDesigner FilterVcf
BamIndexStats FixMateInformation
GatherBamFiles
BedToIntervalList GatherVcfs
BuildBamIndex GenotypeConcordance
CalculateHsMetrics IlluminaBasecallsToFastq
CalculateReadGroupChecksum IlluminaBasecallsToSam
CheckIlluminaDirectory LiftOverIntervalList
CheckTerminatorBlock LiftoverVcf
CleanSam MakeSitesOnlyVcf
CollectAlignmentSummaryMetrics MarkDuplicates
CollectBaseDistributionByCycle MarkDuplicatesWithMateCigar
CollectGcBiasMetrics MarkIlluminaAdapters
CollectHiSeqXPfFailMetrics MeanQualityByCycle
CollectIlluminaBasecallingMetrics MergeBamAlignment
CollectIlluminaLaneMetrics MergeSamFiles
CollectInsertSizeMetrics MergeVcfs
CollectJumpingLibraryMetrics NormalizeFasta
CollectMultipleMetrics PositionBasedDownsampleSam
CollectOxoGMetrics QualityScoreDistribution
CollectQualityYieldMetrics RenameSampleInVcf
CollectRawWgsMetrics ReorderSam
CollectRnaSeqMetrics ReplaceSamHeader
CollectRrbsMetrics RevertOriginalBaseQualitiesAndAddMateCigar
CollectSequencingArtifactMetrics RevertSam
CollectTargetedPcrMetrics SamFormatConverter
CollectVariantCallingMetrics SamToFastq
CollectWgsMetrics ScatterIntervalsByNs
CompareMetrics SortSam
CompareSAMs SortVcf
ConvertSequencingArtifactToOxoG SplitSamByLibrary
CreateSequenceDictionary SplitVcfs
DownsampleSam UpdateVcfSequenceDictionary
EstimateLibraryComplexity ValidateSamFile
ExtractIlluminaBarcodes VcfFormatConverter
ExtractSequences VcfToIntervalList
FastqToSam ViewSam
The package is enhanced by the following packages:
multiqc
Please cite:
Broad Institute:
Picard toolkit.
Broad Institute, GitHub repository
(2019)
Topics: Sequencing; Document, record and content management
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picopore
lossless compression of Nanopore files
|
Versions of package picopore |
Release | Version | Architectures |
trixie | 1.2.0-3 | all |
bullseye | 1.2.0-2 | all |
bookworm | 1.2.0-2 | all |
sid | 1.2.0-3 | all |
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License: DFSG free
|
The Nanopore is a device to determine the sequences of single moleculres
of DNA. No amplification. The output is gigantic and tools like this
one help to reduce it.
Over time, other means have substitute the need for this one. Upstream
has halted development. Some tutorials and pipelines of the Nanopore still
refer to it, though.
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pigx-rnaseq
pipeline for checkpointed and distributed RNA-seq analyses
|
Versions of package pigx-rnaseq |
Release | Version | Architectures |
bullseye | 0.0.10+ds-2 | all |
sid | 0.1.1-1 | all |
trixie | 0.1.1-1 | all |
bookworm | 0.1.0-1.1 | all |
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License: DFSG free
|
This package provides a automated workflow for the automated analysis of
RNA-seq experiments. A series of well-accecpted tools are connected in
Python scripts and controlled via snakemake. This supports the parallel
execution of these workflows and provides checkpointing, such that
interrupted workflows can take up their work again.
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piler
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Versions of package piler |
Release | Version | Architectures |
buster | 0~20140707-2 | amd64,arm64,armhf,i386 |
sid | 0~20140707-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 0~20140707-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 0~20140707-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0~20140707-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0~20140707-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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PILER (Parsimonious Inference of a Library of Elementary Repeats)
searches a genome sequence for repetitive elements. It implements search
algorithms that identify characteristic patterns of local alignments
induced by certain classes of repeats.
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pilercr
software for finding CRISPR repeats
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Versions of package pilercr |
Release | Version | Architectures |
trixie | 1.06+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.06+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.06+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.06+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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CRISPR elements are short, highly conserved repeats in prokaryotic genomes
separated by unique sequences of similar length. PILERCR is designed for the
identification and analysis of CRISPR repeats.
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pilon
automated genome assembly improvement and variant detection tool
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Versions of package pilon |
Release | Version | Architectures |
stretch-backports | 1.22+dfsg-2~bpo9+2 | all |
sid | 1.24-3 | all |
trixie | 1.24-3 | all |
bookworm | 1.24-2 | all |
bullseye | 1.23+dfsg-2 | all |
buster | 1.23+dfsg-1 | all |
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License: DFSG free
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Pilon is a software tool which can be used to:
- Automatically improve draft assemblies
-
Find variation among strains, including large event detection
Pilon requires as input a FASTA file of the genome along with one or more
BAM files of reads aligned to the input FASTA file. Pilon uses read
alignment analysis to identify inconsistencies between the input genome and
the evidence in the reads. It then attempts to make improvements to the
input genome, including:
-
Single base differences
- Small indels
- Larger indel or block substitution events
- Gap filling
- Identification of local misassemblies, including optional opening
of new gaps
Please cite:
Bruce J. Walker, Thomas Abeel, Terrance Shea, Margaret Priest, Amr Abouelliel, Sharadha Sakthikumar, Christina A. Cuomo, Qiandong Zeng, Jennifer Wortman, Sarah K. Young and Ashlee M. Earl:
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement".
(PubMed,eprint)
PLOSone
9(11):e11296
(2014)
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pinfish
Collection of tools to annotate genomes using long read transcriptomics data
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Versions of package pinfish |
Release | Version | Architectures |
bullseye | 0.1.0+ds-2 | amd64,arm64,mips64el,ppc64el,s390x |
bookworm | 0.1.0+ds-3 | amd64,arm64,mips64el,ppc64el,s390x |
trixie | 0.1.0+ds-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.1.0+ds-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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The toolchain is composed of the following tools:
1. spliced_bam2gff - a tool for converting sorted BAM
files containing spliced alignments
into GFF2 format. Each read will be represented as a distinct
transcript. This tool comes handy when visualizing spliced
reads at particular loci and to provide input to the rest
of the toolchain.
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cluster_gff - this tool takes a sorted GFF2 file as
input and clusters together reads having similar
exon/intron structure and creates a rough consensus
of the clusters by taking the median of exon
boundaries from all transcripts in the cluster.
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polish_clusters - this tool takes the cluster
definitions generated by cluster_gff and for each
cluster creates an error corrected read by mapping
all reads on the read with the median length
and polishing it using racon. The polished reads
can be mapped to the genome using minimap2 or GMAP.
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collapse_partials - this tool takes GFFs generated
by either cluster_gff or polish_clusters and filters
out transcripts which are likely to be based on RNA
degradation products from the 5' end. The tool clusters
the input transcripts into "loci" by the 3' ends and
discards transcripts which have a compatible transcripts
in the loci with more exons.
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pique
software pipeline for performing genome wide association studies
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Versions of package pique |
Release | Version | Architectures |
sid | 1.0-7 | all |
trixie | 1.0-7 | all |
bullseye | 1.0-2 | all |
bookworm | 1.0-6 | all |
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License: DFSG free
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PIQUE is a software pipeline for performing genome wide association
studies (GWAS). The main function of PIQUE is to provide ‘convenience’
wrappers that allow users to perform GWAS using the popular program
EMMAX (Kang et al., 2010) without the need to be familiar with all of
the software tools used to generate the required EMMAX input files.
PIQUE will also perform a number of quality control steps prior to
running EMMAX, ensuring that the various input data files are in the
correct format. PIQUE proceeds in two main stages although there are
multiple entry and exit points from which the pipeline can be run. The
first stage consists of running the “pique-input” program, which can
read genotype and phenotype information in several different formats and
generates all the necessary input files required to run EMMAX. The
second step in the pipeline uses the “pique-run” program to actually run
EMMAX using the files generated by “pique-input” (or pre-existing
user-supplied input files) to perform the GWAS and output the analysis
summary files.
The package is enhanced by the following packages:
pique-doc
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pirs
Profile based Illumina pair-end Reads Simulator
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Versions of package pirs |
Release | Version | Architectures |
bookworm | 2.0.2+dfsg-11 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.0.2+dfsg-12 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 2.0.2+dfsg-12 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 2.0.2+dfsg-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.0.2+dfsg-8 | amd64,arm64,armhf,i386 |
stretch | 2.0.2+dfsg-5.1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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The program pIRS can be used for simulating Illumina PE reads, with a
series of characters generated by Illumina sequencing platform, such as
insert size distribution, sequencing error(substitution, insertion,
deletion), quality score and GC content-coverage bias.
The insert size follows a normal distribution, so users should set the
mean value and standard deviation. Usually the standard deviation is set
as 1/20 of the mean value. The normal distribution by Box-Muller method
is simulated.
The program simulates sequencing error, quality score and GC content-
coverage bias according to the empirical distribution profile. Some
default profiles counted from lots of real sequencing data are provided.
To simulate reads from diploid genome, users should simulate the diploid
genome sequence firstly by setting the ratio of heterozygosis SNP,
heterozygosis InDel and structure variation.
Please cite:
Xuesong Hu, Jianying Yuan, Yujian Shi, Jianliang Lu, Binghang Liu, Zhenyu Li, Yanxiang Chen, Desheng Mu, Hao Zhang, Nan Li, Zhen Yue, Fan Bai, Heng Li and Wei Fan:
pIRS: Profile-based Illumina pair-end reads simulator.
(PubMed,eprint)
Bioinformatics
28(11):1533-5
(2012)
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pizzly
Identifies gene fusions in RNA sequencing data
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Versions of package pizzly |
Release | Version | Architectures |
experimental | 0.37.3+ds-10 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.37.3+ds-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.37.3+ds-9 | amd64,arm64,mips64el,ppc64el,s390x |
trixie | 0.37.3+ds-9 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
sid | 0.37.3+ds-9 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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For the interpretation of the transcriptome (the abundance
and sequence of RNA) of tomour cells one is particularly
interested in transcripts that cannot be mapped to single
genes but that are seen to be fused as parts from two genes.
Likely eplanations are chromosomal translocations.
Pizzly can identify novel such peculiarities, building on
interpretations on variable splicing by the tool kallisto.
Both tools are elements of the bcbio workflow.
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placnet
Plasmid Constellation Network project
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Versions of package placnet |
Release | Version | Architectures |
bullseye | 1.03-3 | all |
sid | 1.04-1 | all |
trixie | 1.04-1 | all |
bookworm | 1.04-1 | all |
stretch | 1.03-2 | all |
buster | 1.03-3 | all |
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License: DFSG free
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Placnet is a new tool for plasmid analysis in NGS projects. Placnet is
optimized to work with Illumina sequences but it also works with 454,
Iontorrent or any of the actual sequence technologies.
The input of placnet is a set of contigs and one or more SAM files with
the mapping of the reads against the contigs. Placnet obtains a set of
files, easily opened on Cytoscape software or other network tools.
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plasmidid
mapping-based, assembly-assisted plasmid identification tool
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Versions of package plasmidid |
Release | Version | Architectures |
sid | 1.6.5+dfsg-2 | amd64,arm64 |
trixie | 1.6.5+dfsg-2 | amd64,arm64 |
bookworm | 1.6.5+dfsg-2 | amd64 |
bullseye | 1.6.3+dfsg-3 | amd64 |
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License: DFSG free
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PlasmidID is a mapping-based, assembly-assisted plasmid identification
tool that analyzes and gives graphic solution for plasmid
identification.
PlasmidID is a computational pipeline that maps Illumina reads over
plasmid database sequences. The k-mer filtered, most covered
sequences are clustered by identity to avoid redundancy and the
longest are used as scaffold for plasmid reconstruction. Reads are
assembled and annotated by automatic and specific annotation. All
information generated from mapping, assembly, annotation and local
alignment analyses is gathered and accurately represented in a
circular image which allow user to determine plasmidic composition in
any bacterial sample.
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plasmidomics
draw plasmids and vector maps with PostScript graphics export
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Versions of package plasmidomics |
Release | Version | Architectures |
buster | 0.2.0-7 | all |
jessie | 0.2.0-3 | all |
bookworm | 0.2.0-10 | all |
bullseye | 0.2.0-9 | all |
sid | 0.2.0-10 | all |
trixie | 0.2.0-10 | all |
stretch | 0.2.0-5 | all |
Debtags of package plasmidomics: |
field | biology, biology:molecular |
interface | x11 |
role | program |
scope | utility |
uitoolkit | tk |
works-with | image:vector |
works-with-format | postscript |
x11 | application |
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License: DFSG free
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Plasmidomics is written for easy drawing of plasmids and vector maps
to use them in theses, presentations or other forms of publications. It
natively supports PostScript as output format.
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plasmidseeker
identification of known plasmids from whole-genome sequencing reads
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Versions of package plasmidseeker |
Release | Version | Architectures |
bookworm | 1.3+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.3+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.3+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.3+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.0+dfsg-1 | amd64,arm64,armhf,i386 |
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License: DFSG free
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PlasmidSeeker is a k-mer based program for the identification of known
plasmids from bacterial whole genome sequencing reads.
PlasmidSeeker that enables the detection of plasmids from bacterial WGS
data without read assembly. The PlasmidSeeker algorithm is based on
k-mers and uses k-mer abundance to distinguish between plasmid and
bacterial sequences. The performance of PlasmidSeeker was tested on a set
of simulated and real bacterial WGS samples, resulting in 100%
sensitivity and 99.98% specificity.
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plast
Parallel Local Sequence Alignment Search Tool
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Versions of package plast |
Release | Version | Architectures |
buster | 2.3.2+dfsg-1 | amd64 |
stretch | 2.3.1+dfsg-4 | amd64 |
sid | 2.3.2+dfsg-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.3.2+dfsg-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.3.2+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.3.2+dfsg-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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PLAST is a fast, accurate and NGS scalable bank-to-bank sequence
similarity search tool providing significant accelerations of seeds-
based heuristic comparison methods, such as the Blast suite of
algorithms.
Relying on unique software architecture, PLAST takes full advantage of
recent multi-core personal computers without requiring any additional
hardware devices.
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plink
whole-genome association analysis toolset
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Versions of package plink |
Release | Version | Architectures |
bookworm | 1.07+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.07+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.07+dfsg-2 | amd64,arm64,armhf,i386 |
jessie | 1.07-3 | amd64,armel,armhf,i386 |
stretch | 1.07-7 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.07+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.07+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package plink: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
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License: DFSG free
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plink expects as input the data from SNP (single
nucleotide polymorphism) chips of many individuals
and their phenotypical description of a disease.
It finds associations of single or pairs of DNA
variations with a phenotype and can retrieve
SNP annotation from an online source.
SNPs can evaluated individually or as pairs for their
association with the disease phenotypes. The joint
investigation of copy number variations is supported.
A variety of statistical tests have been implemented.
Please note: The executable was renamed to plink1
because of a name clash. Please read more about this
in /usr/share/doc/plink/README.Debian.
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plink1.9
whole-genome association analysis toolset
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Versions of package plink1.9 |
Release | Version | Architectures |
buster | 1.90~b6.6-181012-1 | amd64,armhf,i386 |
bookworm | 1.90~b6.26-220402-1 | amd64,armel,armhf,i386,mipsel |
trixie | 1.90~b7.2-231211-1 | amd64,armel,armhf,i386 |
bullseye | 1.90~b6.21-201019-1 | amd64,armel,armhf,i386,mipsel |
stretch | 1.90~b3.45-170113-1 | amd64,armel,armhf,i386,mipsel |
sid | 1.90~b7.2-231211-1 | amd64,armel,armhf,i386 |
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License: DFSG free
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plink expects as input the data from SNP (single nucleotide polymorphism)
chips of many individuals and their phenotypical description of a disease.
It finds associations of single or pairs of DNA variations with a phenotype
and can retrieve SNP annotation from an online source.
SNPs can evaluated individually or as pairs for their association with the
disease phenotypes. The joint investigation of copy number variations is
supported. A variety of statistical tests have been implemented.
plink1.9 is a comprehensive update of plink with new algorithms and new
methods, faster and less memory consumer than the first plink.
Please note: The executable was renamed to plink1.9
because of a name clash. Please read more about this
in /usr/share/doc/plink1.9/README.Debian.
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plink2
whole-genome association analysis toolset
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Versions of package plink2 |
Release | Version | Architectures |
sid | 2.00~a5.8-231123+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 2.00~a5.8-231123+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.00~a3.5-220809+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.00~a3-210203+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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plink expects as input the data from SNP (single nucleotide polymorphism)
chips of many individuals and their phenotypical description of a disease.
It finds associations of single or pairs of DNA variations with a phenotype
and can retrieve SNP annotation from an online source.
SNPs can evaluated individually or as pairs for their association with the
disease phenotypes. The joint investigation of copy number variations is
supported. A variety of statistical tests have been implemented.
plink2 is a comprehensive update of plink and plink1.9 with new algorithms
and new methods, faster and less memory consumer than the first plink.
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plip
fully automated protein-ligand interaction profiler
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Versions of package plip |
Release | Version | Architectures |
stretch | 1.3.3+dfsg-1 | all |
bullseye | 2.1.7+dfsg-1 | all |
sid | 2.3.0+dfsg-2 | all |
bookworm | 2.2.2+dfsg-1 | all |
trixie | 2.3.0+dfsg-2 | all |
buster | 1.4.3~b+dfsg-2 | all |
upstream | 2.4.0 |
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License: DFSG free
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The Protein-Ligand Interaction Profiler (PLIP) is a tool to analyze
and visualize protein-ligand interactions in PDB files.
Features include:
- Detection of eight different types of noncovalent interactions
- Automatic detection of relevant ligands in a PDB file
- Direct download of PDB structures from wwPDB server if valid
PDB ID is given
- Processing of custom PDB files containing protein-ligand complexes
(e.g. from docking)
- No need for special preparation of a PDB file, works out of the box
- Atom-level interaction reports in rST and XML formats for easy parsing
- Generation of PyMOL session files (.pse) for each pairing, enabling easy
preparation of images for publications and talks
- Rendering of preview image for each ligand and its interactions
with the protein
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poa
Partial Order Alignment for multiple sequence alignment
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Versions of package poa |
Release | Version | Architectures |
stretch | 2.0+20060928-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2.0+20060928-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 2.0+20060928-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.0+20060928-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.0+20060928-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.0+20060928-7 | amd64,arm64,armhf,i386 |
jessie | 2.0+20060928-3 | amd64,armel,armhf,i386 |
Debtags of package poa: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
works-with-format | plaintext |
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License: DFSG free
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POA is Partial Order Alignment, a fast program for multiple sequence
alignment (MSA) in bioinformatics. Its advantages are speed,
scalability, sensitivity, and the superior ability to handle branching
/ indels in the alignment. Partial order alignment is an approach to
MSA, which can be combined with existing methods such as progressive
alignment. POA optimally aligns a pair of MSAs and which therefore can
be applied directly to progressive alignment methods such as CLUSTAL.
For large alignments, Progressive POA is 10-30 times faster than
CLUSTALW.
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populations
population genetic software
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Versions of package populations |
Release | Version | Architectures |
buster | 1.2.33+svn0120106+dfsg-2 | amd64,arm64,armhf,i386 |
bullseye | 1.2.33+svn0120106+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.2.33+svn0120106+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.2.33+svn0120106+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.2.33+svn0120106+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.2.33+svn0120106-2.1 | amd64,armel,armhf,i386 |
stretch | 1.2.33+svn0120106-2.1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package populations: |
role | program |
uitoolkit | qt |
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License: DFSG free
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Populations is a population genetic software. It computes genetic
distances between populations or individuals. It builds phylogenetic
trees (NJ or UPGMA) with bootstrap values.
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porechop
adapter trimmer for Oxford Nanopore reads
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Versions of package porechop |
Release | Version | Architectures |
bullseye | 0.2.4+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
experimental | 0.2.4+dfsg-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.2.4+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.2.4+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 0.2.4+dfsg-1 | amd64,arm64,armhf,i386 |
bookworm | 0.2.4+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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Porechop is a tool for finding and removing adapters from Oxford
Nanopore reads. Adapters on the ends of reads are trimmed off, and
when a read has an adapter in its middle, it is treated as chimeric
and chopped into separate reads. Porechop performs thorough
alignments to effectively find adapters, even at low sequence
identity.
Porechop also supports demultiplexing of Nanopore reads that were
barcoded with the Native Barcoding Kit, PCR Barcoding Kit or Rapid
Barcoding Kit.
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poretools
toolkit for nanopore nucleotide sequencing data
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Versions of package poretools |
Release | Version | Architectures |
sid | 0.6.0+dfsg-7 | all |
trixie | 0.6.0+dfsg-7 | all |
bookworm | 0.6.0+dfsg-6 | all |
bullseye | 0.6.0+dfsg-5 | all |
buster | 0.6.0+dfsg-3 | all |
stretch | 0.6.0+dfsg-2 | all |
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License: DFSG free
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poretools is a flexible toolkit for exploring datasets generated by nanopore
sequencing devices from MinION for the purposes of quality control and
downstream analysis. Poretools operates directly on the native FAST5 (a
variant of the HDF5 standard) file format produced by ONT and provides a
wealth of format conversion utilities and data exploration and visualization
tools.
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pplacer
phylogenetic placement and downstream analysis
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Versions of package pplacer |
Release | Version | Architectures |
sid | 1.1~alpha19-8 | amd64,arm64,ppc64el,riscv64,s390x |
bullseye | 1.1~alpha19-4 | amd64,arm64,ppc64el,s390x |
|
License: DFSG free
|
Pplacer places reads on a phylogenetic tree. guppy (Grand Unified
Phylogenetic Placement Yanalyzer) yanalyzes them. rppr is a helpful tool
for working with reference packages.
Pplacer places query sequences on a fixed reference phylogenetic tree to
maximize phylogenetic likelihood or posterior probability according to a
reference alignment. Pplacer is designed to be fast, to give useful
information about uncertainty, and to offer advanced visualization and
downstream analysis.
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prank
Probabilistic Alignment Kit for DNA, codon and amino-acid sequences
|
Versions of package prank |
Release | Version | Architectures |
buster | 0.0.170427+dfsg-2 | amd64,arm64,armhf,i386 |
jessie | 0.0.140110-1 | amd64,armel,armhf,i386 |
stretch | 0.0.150803-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 0.0.170427+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.0.170427+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.0.170427+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.0.170427+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
PRANK is a probabilistic multiple alignment program for DNA, codon
and amino-acid sequences. It's based on a novel algorithm that treats
insertions correctly and avoids over-estimation of the number of
deletion events. In addition, PRANK borrows ideas from maximum
likelihood methods used in phylogenetics and correctly takes into
account the evolutionary distances between sequences. Lastly, PRANK
allows for defining a potential structure for sequences to be aligned
and then, simultaneously with the alignment, predicts the locations
of structural units in the sequences.
PRANK is a command-line program for UNIX-style environments but the
same sequence alignment engine is implemented in the graphical
program PRANKSTER. In addition to providing a user-friendly interface
to those not familiar with Unix systems, PRANKSTER is an alignment
browser for alignments saved in the HSAML format. The novel format
allows for storing all the information generated by the aligner and
the alignment browser is a convenient way to analyse and manipulate
the data.
PRANK aims at an evolutionarily correct sequence alignment and often
the result looks different from ones generated with other alignment
methods. There are, however, cases where the different look is caused
by violations of the method's assumptions. To understand why things
may go wrong and how to avoid that, read this explanation of
differences between PRANK and traditional progressive alignment
methods.
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predictnls
prediction and analysis of protein nuclear localization signals
|
Versions of package predictnls |
Release | Version | Architectures |
bookworm | 1.0.20-8 | all |
buster | 1.0.20-5 | all |
jessie | 1.0.20-1 | all |
trixie | 1.0.20-8 | all |
stretch | 1.0.20-3 | all |
bullseye | 1.0.20-6 | all |
sid | 1.0.20-8 | all |
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License: DFSG free
|
predictnls is a method for the prediction and analysis of protein nuclear
localization signals (NLS). In addition to reporting the positions of
NLSs found, predictnls also gives short statistics.
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presto
toolkit for processing B and T cell sequences
|
Versions of package presto |
Release | Version | Architectures |
trixie | 0.7.2-2 | all |
sid | 0.7.2-2 | all |
bookworm | 0.7.1-1 | all |
bullseye | 0.6.2-1 | all |
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License: DFSG free
|
pRESTO is a toolkit for processing raw reads from high-throughput
sequencing of B cell and T cell repertoires.
Dramatic improvements in high-throughput sequencing technologies now
enable large-scale characterization of lymphocyte repertoires, defined
as the collection of trans-membrane antigen-receptor proteins located on
the surface of B cells and T cells. The REpertoire Sequencing TOolkit
(pRESTO) is composed of a suite of utilities to handle all stages
of sequence processing prior to germline segment assignment. pRESTO
is designed to handle either single reads or paired-end reads. It
includes features for quality control, primer masking, annotation of
reads with sequence embedded barcodes, generation of unique molecular
identifier (UMI) consensus sequences, assembly of paired-end reads and
identification of duplicate sequences. Numerous options for sequence
sorting, sampling and conversion operations are also included.
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prime-phylo
bayesian estimation of gene trees taking the species tree into account
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Versions of package prime-phylo |
Release | Version | Architectures |
sid | 1.0.11-13 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
jessie | 1.0.11-2 | amd64,armel,armhf,i386 |
stretch | 1.0.11-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.11-7 | amd64,arm64,armhf,i386 |
bullseye | 1.0.11-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.0.11-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.0.11-13 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
|
PrIME (Probabilistic Integrated Models of Evolution) is a package
supporting inference of evolutionary parameters in a Bayesian framework
using Markov chain Monte Carlo simulation. A distinguishing feature of
PrIME is that the species tree is taken into account when analyzing gene
trees.
The input data to PrIME is a multiple sequence alignment in FASTA format
and the output data contains trees in Newick format.
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primer3
tool to design flanking oligo nucleotides for DNA amplification
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Versions of package primer3 |
Release | Version | Architectures |
trixie | 2.6.1-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 2.3.7-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.3.6-1 | amd64,armel,armhf,i386 |
buster | 2.4.0-2 | amd64,arm64,armhf,i386 |
bullseye | 2.4.0-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.6.1-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.6.1-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package primer3: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
works-with-format | plaintext |
|
License: DFSG free
|
Primer3 picks primers for Polymerase Chain Reactions (PCRs), considering as
criteria oligonucleotide melting temperature, size, GC content and
primer-dimer possibilities, PCR product size, positional constraints within
the source sequence, and miscellaneous other constraints. All of these
criteria are user-specifiable as constraints, and some are specifiable as
terms in an objective function that characterizes an optimal primer pair.
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prinseq-lite
PReprocessing and INformation of SEQuence data (lite version)
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Versions of package prinseq-lite |
Release | Version | Architectures |
bullseye | 0.20.4-6 | all |
sid | 0.20.4-6 | all |
trixie | 0.20.4-6 | all |
bookworm | 0.20.4-6 | all |
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License: DFSG free
|
PRINSEQ will help you to preprocess your genomic or metagenomic sequence data
in FASTA or FASTQ format. It is a tool that generates summary statistics of
sequence and quality data and that is used to filter, reformat and trim
next-generation sequence data. It is particular designed for 454/Roche data,
but can also be used for other types of sequence data. The standalone version
is primarily designed for data preprocessing and does not generate summary
statistics in graphical form.
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proalign
Probabilistic multiple alignment program
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Versions of package proalign |
Release | Version | Architectures |
trixie | 0.603-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 0.603-1 | amd64,armel,armhf,i386 |
stretch | 0.603-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.603-4 | amd64,arm64,armhf,i386 |
bullseye | 0.603-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.603-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.603-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
|
ProAlign performs probabilistic sequence alignments using hidden Markov
models (HMM). It includes a graphical interface (GUI) allowing to (i)
perform alignments of nucleotide or amino-acid sequences, (ii) view the
quality of solutions, (iii) filter the unreliable alignment regions and
(iv) export alignments to other software.
ProAlign uses a progressive method, such that multiple alignment is
created stepwise by performing pairwise alignments in the nodes of a
guide tree. Sequences are described with vectors of character
probabilities, and each pairwise alignment reconstructs the ancestral
(parent) sequence by computing the probabilities of different
characters according to an evolutionary model.
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probabel
Toolset for Genome-Wide Association Analysis
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Versions of package probabel |
Release | Version | Architectures |
jessie | 0.4.3-2 | amd64,armel,armhf,i386 |
bookworm | 0.5.0+dfsg-6 | amd64,i386 |
trixie | 0.5.0+dfsg-6 | amd64,i386 |
sid | 0.5.0+dfsg-6 | amd64,i386 |
bullseye | 0.5.0+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.5.0+dfsg-3 | amd64,arm64,armhf,i386 |
stretch | 0.4.5-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
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License: DFSG free
|
The ProbABEL package is part of the GenABEL project for analysis of genome-wide
data. ProbABEL is used to run GWAS. Using files in filevector/DatABEL format
even allows for running GWAS on computers with only a few GB of RAM.
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probalign
multiple sequence alignment using partition function posterior probabilities
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Versions of package probalign |
Release | Version | Architectures |
bullseye | 1.4-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.4-8 | amd64,arm64,armhf,i386 |
stretch | 1.4-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.4-3 | amd64,armel,armhf,i386 |
sid | 1.4-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.4-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.4-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
Probalign uses partition function posterior probability estimates to
compute maximum expected accuracy multiple sequence alignments. It
performs statistically significantly better than the leading alignment
programs Probcons v1.1, MAFFT v5.851, and MUSCLE v3.6 on BAliBASE 3.0,
HOMSTRAD, and OXBENCH benchmarks. Probalign improvements are largest on
datasets containing N/C terminal extensions and on datasets with long
and heterogeneous length sequences. On heteregeneous length datasets
containing repeats Probalign alignment accuracy is 10% and 15% higher
than the other three methods when standard deviation of length is at
least 300 and 400.
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probcons
PROBabilistic CONSistency-based multiple sequence alignment
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Versions of package probcons |
Release | Version | Architectures |
jessie | 1.12-9 | amd64,armel,armhf,i386 |
stretch | 1.12-11 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.12-12 | amd64,arm64,armhf,i386 |
bullseye | 1.12-13 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.12-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.12-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.12-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package probcons: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | comparing |
works-with-format | plaintext |
|
License: DFSG free
|
Tool for generating multiple alignments of protein sequences. Using a
combination of probabilistic modeling and consistency-based alignment
techniques, PROBCONS has achieved the highest accuracies of all alignment
methods to date. On the BAliBASE benchmark alignment database, alignments
produced by PROBCONS show statistically significant improvement over current
programs, containing an average of 7% more correctly aligned columns than
those of T-Coffee, 11% more correctly aligned columns than those of CLUSTAL W,
and 14% more correctly aligned columns than those of DIALIGN.
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proda
multiple alignment of protein sequences
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Versions of package proda |
Release | Version | Architectures |
trixie | 1.0-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.0-13 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.0-12 | amd64,arm64,armhf,i386 |
bullseye | 1.0-13 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.0-10 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.0-8 | amd64,armel,armhf,i386 |
sid | 1.0-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package proda: |
biology | nuceleic-acids, peptidic |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing, comparing |
works-with-format | plaintext |
|
License: DFSG free
|
ProDA is a system for automated detection and alignment of homologous
regions in collections of proteins with arbitrary domain architectures.
Given an input set of unaligned sequences, ProDA identifies all
homologous regions appearing in one or more sequences, and returns a
collection of local multiple alignments for these regions.
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prodigal
Microbial (bacterial and archaeal) gene finding program
|
Versions of package prodigal |
Release | Version | Architectures |
buster | 2.6.3-4 | amd64,arm64,armhf,i386 |
jessie | 2.6.1-1 | amd64,armel,i386 |
trixie | 2.6.3-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.6.3-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 2.6.3-1 | amd64,arm64,armel,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.6.3-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.6.3-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a
microbial (bacterial and archaeal) gene finding program developed at
Oak Ridge National Laboratory and the University of Tennessee.
Key features of Prodigal include:
Speed: Prodigal is an extremely fast gene recognition tool
(written in very vanilla C). It can analyze an entire microbial genome
in 30 seconds or less.
Accuracy: Prodigal is a highly accurate gene finder.
It correctly locates the 3' end of every gene in the experimentally verified
Ecogene data set (except those containing introns).
It possesses a very sophisticated ribosomal binding site scoring system that
enables it to locate the translation initiation site with great accuracy
(96% of the 5' ends in the Ecogene data set are located correctly).
Specificity: Prodigal's false positive rate compares favorably with other
gene identification programs, and usually falls under 5%.
GC-Content Indifferent: Prodigal performs well even in high GC genomes,
with over a 90% perfect match (5'+3') to the Pseudomonas aeruginosa curated
annotations.
Metagenomic Version: Prodigal can run in metagenomic mode and analyze
sequences even when the organism is unknown.
Ease of Use: Prodigal can be run in one step on a single genomic sequence
or on a draft genome containing many sequences. It does not need to be
supplied with any knowledge of the organism, as it learns all the properties
it needs to on its own.
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profbval
predictor of flexible/rigid protein residues from sequence
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Versions of package profbval |
Release | Version | Architectures |
buster | 1.0.22-6 | all |
sid | 1.0.22-8 | all |
trixie | 1.0.22-8 | all |
jessie | 1.0.22-1 | all |
stretch | 1.0.22-4 | all |
bookworm | 1.0.22-8 | all |
bullseye | 1.0.22-7 | all |
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License: DFSG free
|
PROFbval can be useful for both protein structure and
function predictions. For instance, a biologist can locate potentially
antigenic determinants by identifying the most flexible residues on the
protein surface. Additionally, a crystallographer can locate residues that
potentially have high experimental B-values.
PROFbval takes the following input, further described on profbval(1):
- a protein sequence in a FASTA file
- secondary structure and solvent accessibility prediction by prof(1)
- an HSSP file
Background: the mobility of a given residue on the protein surface is related
to its functional role.
Therefore, identification of extremely rigid or flexible
residues on the protein surface is helpful for identifying functionally
important residues in proteins. A common measure of atom mobility in proteins
is B-value data from x-ray crystallography structures. PROFbval is the first
tool to predict normalized backbone B-values from amino-acid sequence.
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profisis
prediction of protein-protein interaction sites from sequence
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Versions of package profisis |
Release | Version | Architectures |
stretch | 1.0.11-3 | all |
jessie | 1.0.11-1 | all |
bullseye | 1.0.11-6 | all |
bookworm | 1.0.11-7 | all |
buster | 1.0.11-5 | all |
sid | 1.0.11-7 | all |
trixie | 1.0.11-7 | all |
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License: DFSG free
|
Profisis (ISIS) identifies interacting protein residues in protein-protein
interfaces from sequence alone.
The strongest predictions of the method reached over 90% accuracy in a
cross-validation experiment.
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profnet-bval
neural network architecture for profbval
|
Versions of package profnet-bval |
Release | Version | Architectures |
trixie | 1.0.22-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.0.22-6 | amd64,arm64,armhf,i386 |
sid | 1.0.22-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.0.22-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.0.22-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.0.22-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.0.22-2 | amd64,armel,armhf,i386 |
|
License: DFSG free
|
Profnet is a component of the prediction methods that make up the
Predict Protein service by the lab of Burkhard Rost. It provides the neural
network component to a variety of predictors that perform protein feature
prediction directly from sequence. This neural network implementation has
to be compiled for every different network architecture.
This package contains the neural network architecture for profbval.
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profnet-chop
neural network architecture for profchop
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Versions of package profnet-chop |
Release | Version | Architectures |
jessie | 1.0.22-2 | amd64,armel,armhf,i386 |
sid | 1.0.22-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.0.22-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.22-6 | amd64,arm64,armhf,i386 |
stretch | 1.0.22-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.0.22-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.0.22-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
Profnet is a component of the prediction methods that make up the
Predict Protein service by the lab of Burkhard Rost. It provides the neural
network component to a variety of predictors that perform protein feature
prediction directly from sequence. This neural network implementation has
to be compiled for every different network architecture.
This package contains the neural network architecture for profchop.
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profnet-con
neural network architecture for profcon
|
Versions of package profnet-con |
Release | Version | Architectures |
bullseye | 1.0.22-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.0.22-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.22-6 | amd64,arm64,armhf,i386 |
jessie | 1.0.22-2 | amd64,armel,armhf,i386 |
trixie | 1.0.22-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.0.22-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.0.22-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
Profnet is a component of the prediction methods that make up the
Predict Protein service by the lab of Burkhard Rost. It provides the neural
network component to a variety of predictors that perform protein feature
prediction directly from sequence. This neural network implementation has
to be compiled for every different network architecture.
This package contains the neural network architecture for profcon.
|
|
profnet-isis
neural network architecture for profisis
|
Versions of package profnet-isis |
Release | Version | Architectures |
sid | 1.0.22-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.0.22-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.0.22-6 | amd64,arm64,armhf,i386 |
jessie | 1.0.22-2 | amd64,armel,armhf,i386 |
bullseye | 1.0.22-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.0.22-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.0.22-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
Profnet is a component of the prediction methods that make up the
Predict Protein service by the lab of Burkhard Rost. It provides the neural
network component to a variety of predictors that perform protein feature
prediction directly from sequence. This neural network implementation has
to be compiled for every different network architecture.
This package contains the neural network architecture for profisis.
|
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profnet-md
neural network architecture for metadisorder
|
Versions of package profnet-md |
Release | Version | Architectures |
bookworm | 1.0.22-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.0.22-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.0.22-2 | amd64,armel,armhf,i386 |
bullseye | 1.0.22-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.22-6 | amd64,arm64,armhf,i386 |
trixie | 1.0.22-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.0.22-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
|
Profnet is a component of the prediction methods that make up the
Predict Protein service by the lab of Burkhard Rost. It provides the neural
network component to a variety of predictors that perform protein feature
prediction directly from sequence. This neural network implementation has
to be compiled for every different network architecture.
This package contains the neural network architecture for metadisorder.
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profnet-norsnet
neural network architecture for norsnet
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Versions of package profnet-norsnet |
Release | Version | Architectures |
trixie | 1.0.22-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.0.22-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.22-6 | amd64,arm64,armhf,i386 |
stretch | 1.0.22-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.0.22-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.0.22-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.0.22-2 | amd64,armel,armhf,i386 |
|
License: DFSG free
|
Profnet is a component of the prediction methods that make up the
Predict Protein service by the lab of Burkhard Rost. It provides the neural
network component to a variety of predictors that perform protein feature
prediction directly from sequence. This neural network implementation has
to be compiled for every different network architecture.
This package contains the neural network architecture for norsnet.
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profnet-prof
neural network architecture for profacc
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Versions of package profnet-prof |
Release | Version | Architectures |
jessie | 1.0.22-2 | amd64,armel,armhf,i386 |
buster | 1.0.22-6 | amd64,arm64,armhf,i386 |
stretch | 1.0.22-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.0.22-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.0.22-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.0.22-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.0.22-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
Profnet is a component of the prediction methods that make up the
Predict Protein service by the lab of Burkhard Rost. It provides the neural
network component to a variety of predictors that perform protein feature
prediction directly from sequence. This neural network implementation has
to be compiled for every different network architecture.
This package contains the neural network architecture for profsec and profacc.
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profnet-snapfun
neural network architecture for snapfun
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Versions of package profnet-snapfun |
Release | Version | Architectures |
stretch | 1.0.22-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.0.22-2 | amd64,armel,armhf,i386 |
buster | 1.0.22-6 | amd64,arm64,armhf,i386 |
bookworm | 1.0.22-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.0.22-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.0.22-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.0.22-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
Profnet is a component of the prediction methods that make up the
Predict Protein service by the lab of Burkhard Rost. It provides the neural
network component to a variety of predictors that perform protein feature
prediction directly from sequence. This neural network implementation has
to be compiled for every different network architecture.
This package contains the neural network architecture for snapfun.
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profphd
secondary structure and solvent accessibility predictor
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Versions of package profphd |
Release | Version | Architectures |
buster | 1.0.42-3 | all |
jessie | 1.0.40-1 | all |
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License: DFSG free
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This package provides prof(1), the protein secondary structure, accessibility
and transmembrane helix predictor from Burkhard Rost. Prediction is either
done from protein sequence alone or from an alignment - the latter should be
used for optimal performance.
How well does prof(1) perform?
-
Secondary structure is predicted at an expected average accuracy > 72% for
the three states helix, strand and loop.
-
Solvent accessibility is predicted at a correlation coefficient
(correlation between experimentally observed and predicted relative
solvent accessibility) of 0.54
-
Transmembrane helix prediction has an expected per-residue accuracy of
about 95%. The number of false positives, i.e., transmembrane helices
predicted in globular proteins, is about 2%.
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profphd-net
neural network architecture for profphd
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Versions of package profphd-net |
Release | Version | Architectures |
stretch | 1.0.22-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 1.0.22-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.0.22-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.0.22-6 | amd64,arm64,armhf,i386 |
bookworm | 1.0.22-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.0.22-2 | amd64,armel,armhf,i386 |
bullseye | 1.0.22-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
Profnet is a component of the prediction methods that make up the
Predict Protein service by the lab of Burkhard Rost. It provides the neural
network component to a variety of predictors that perform protein feature
prediction directly from sequence. This neural network implementation has
to be compiled for every different network architecture.
This package contains the neural network architecture for profphd.
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profphd-utils
profphd helper utilities convert_seq and filter_hssp
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Versions of package profphd-utils |
Release | Version | Architectures |
sid | 1.0.10-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.0.10-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.0.10-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.0.10-1 | amd64,armel,armhf,i386 |
buster | 1.0.10-5 | amd64,arm64,armhf,i386 |
trixie | 1.0.10-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.0.10-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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The package provides the following binary utilities: convert_seq, filter_hssp.
These are used by prof from the profphd package: a secondary structure,
accessibility and transmembrane helix predictor from Burkhard Rost.
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proftmb
per-residue prediction of bacterial transmembrane beta barrels
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Versions of package proftmb |
Release | Version | Architectures |
buster | 1.1.12-8 | amd64,arm64,armhf,i386 |
bookworm | 1.1.12-11 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.1.12-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.1.12-2 | amd64,armel,armhf,i386 |
sid | 1.1.12-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.1.12-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.1.12-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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proftmb predicts transmembrane beta-barrel (TMB) proteins in Gram-negative
bacteria.
For each query protein, proftmb provides both a Z-value indicating that the
protein actually contains a membrane barrel, and a four-state per-residue
labeling of upward- and downward-facing strands, periplasmic hairpins and
extracellular loops.
The package is enhanced by the following packages:
proftmb-dbg
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progressivemauve
multiple genome alignment algorithms
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Versions of package progressivemauve |
Release | Version | Architectures |
sid | 1.2.0+4713+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.2.0+4713-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.2.0+4713+dfsg-4 | amd64,arm64,armhf,i386 |
bullseye | 1.2.0+4713+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.2.0+4713+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.2.0+4713+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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The mauveAligner and progressiveMauve alignment algorithms have been
implemented as command-line programs included with the downloadable Mauve
software. When run from the command-line, these programs provide options
not yet available in the graphical interface.
Mauve is a system for efficiently constructing multiple genome alignments
in the presence of large-scale evolutionary events such as rearrangement
and inversion. Multiple genome alignment provides a basis for research
into comparative genomics and the study of evolutionary dynamics. Aligning
whole genomes is a fundamentally different problem than aligning short
sequences.
Mauve has been developed with the idea that a multiple genome aligner
should require only modest computational resources. It employs algorithmic
techniques that scale well in the amount of sequence being aligned. For
example, a pair of Y. pestis genomes can be aligned in under a minute,
while a group of 9 divergent Enterobacterial genomes can be aligned in
a few hours.
Mauve computes and interactively visualizes genome sequence comparisons.
Using FastA or GenBank sequence data, Mauve constructs multiple genome
alignments that identify large-scale rearrangement, gene gain, gene loss,
indels, and nucleotide substutition.
Mauve is developed at the University of Wisconsin.
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prokka
rapid annotation of prokaryotic genomes
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Versions of package prokka |
Release | Version | Architectures |
bookworm | 1.14.6+dfsg-4 | amd64 |
trixie | 1.14.6+dfsg-6 | all |
bullseye | 1.14.6+dfsg-3 | amd64 |
sid | 1.14.6+dfsg-6 | all |
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License: DFSG free
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A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a
quad-core computer, and scales well to 32 core SMP systems. It produces GFF3,
GBK and SQN files that are ready for editing in Sequin and ultimately submitted
to Genbank/DDJB/ENA.
The package is enhanced by the following packages:
multiqc
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proteinortho
Detection of (Co-)orthologs in large-scale protein analysis
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Versions of package proteinortho |
Release | Version | Architectures |
buster | 5.16.b+dfsg-1 | amd64,arm64,armhf,i386 |
sid | 6.3.1+dfsg-1 | amd64,arm64,ppc64el,riscv64,s390x |
trixie | 6.3.1+dfsg-1 | amd64,arm64,ppc64el,riscv64,s390x |
bullseye | 6.0.28+dfsg-1 | amd64,arm64,ppc64el,s390x |
bookworm | 6.1.7+dfsg-1 | amd64,arm64,ppc64el,s390x |
stretch | 5.15+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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Proteinortho is a stand-alone tool that is geared towards large datasets
and makes use of distributed computing techniques when run on multi-core
hardware. It implements an extended version of the reciprocal best
alignment heuristic. Proteinortho was applied to compute orthologous
proteins in the complete set of all 717 eubacterial genomes available at
NCBI at the beginning of 2009. Authors succeeded identifying thirty
proteins present in 99% of all bacterial proteomes.
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prottest
selection of best-fit models of protein evolution
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Versions of package prottest |
Release | Version | Architectures |
stretch | 3.4.2+dfsg-2 | all |
buster | 3.4.2+dfsg-3 | all |
bullseye | 3.4.2+dfsg-5 | all |
bookworm | 3.4.2+dfsg-8 | all |
trixie | 3.4.2+dfsg-8 | all |
sid | 3.4.2+dfsg-8 | all |
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License: DFSG free
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PROTTEST (ModelTest's relative) is a program for selecting the model of
protein evolution that best fits a given set of sequences (alignment).
This java program is based on the Phyml program (for maximum likelihood
calculations and optimization of parameters) and uses the PAL library as
well. Models included are empirical substitution matrices (such as WAG,
LG, mtREV, Dayhoff, DCMut, JTT, VT, Blosum62, CpREV, RtREV, MtMam,
MtArt, HIVb, and HIVw) that indicate relative rates of amino acid
replacement, and specific improvements (+I:invariable sites, +G: rate
heterogeneity among sites, +F: observed amino acid frequencies) to
account for the evolutionary constraints impossed by conservation of
protein structure and function. ProtTest uses the Akaike Information
Criterion (AIC) and other statistics (AICc and BIC) to find which of the
candidate models best fits the data at hand.
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provean
Protein Variation Effect Analyzer
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Versions of package provean |
Release | Version | Architectures |
sid | 1.1.5+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.1.5+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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PROVEAN (Protein Variation Effect Analyzer) is a software tool which predicts
whether an amino acid substitution or indel has an impact on the biological
function of a protein.
PROVEAN is useful for filtering sequence variants to identify nonsynonymous or
indel variants that are predicted to be functionally important.
The performance of PROVEAN is comparable to popular tools such as SIFT or
PolyPhen-2.
A fast computation approach to obtain pairwise sequence alignment scores
enabled the generation of precomputed PROVEAN predictions for 20 single AA
substitutions and a single AA deletion at every amino acid position of all
protein sequences in human and mouse.
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pscan-chip
ChIP-based identifcation of TF binding sites
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Versions of package pscan-chip |
Release | Version | Architectures |
bookworm | 1.1-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.1-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.1-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.1-2 | amd64,arm64,armhf,i386 |
bullseye | 1.1-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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Regulation of transcription is one of the main check points of gene
expression regulation and plays a key role in fundamental processes like
cellular differentiation and dynamic molecular responses to stimuli The
transcriptional activity of genes is finely regulated by the interaction
of sequence elements on the DNA (transcription factor binding sites or
TFBSs) and particular proteins called Transcription Factors (TFs).
,
TFBSs are usually clustered in specific regulatory genomic regions
called promoters and enhancers. TFs usually recognize TFBSs in a loose
sequence specific fashion but there is no computational way to determine
if any given sequence motif on the DNA is actually bound in-vivo by a
TF, even when the motif is an istance of the sequences typically bound
by the TF itself.
Tools like Pscan and PscanChIP analyse a set of regulatory sequences
to detect motif enrichment. The rationale is that if a given TFBS is
present in a "surpisingly high" number of istances then there is a good
chance that the TF that recognize that motif is a common regulator of
the input sequences, thus they use redundancy as an information source.
While Pscan (of the pscan-tfbs package) is tailored to work on promoters,
that is the regulatory regions upstream of transcription start sites,
PscanChIP is suited to work on more general regulatory genomic regions
like the ones identified through ChIP-Seq experiments.
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pscan-tfbs
search for transcription factor binding sites
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Versions of package pscan-tfbs |
Release | Version | Architectures |
bullseye | 1.2.2-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.2.2-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.2.2-3 | amd64,arm64,armhf,i386 |
sid | 1.2.2-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.2.2-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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Pscan finds Over-represented Transcription Factor Binding Site Motifs in
Sequences from Co-Regulated or Co-Expressed Genes.
Pscan is a software tool that scans a set of sequences (e.g. promoters)
from co-regulated or co-expressed genes with motifs describing the
binding specificity of known transcription factors and assesses which
motifs are significantly over- or under-represented, providing thus
hints on which transcription factors could be common regulators of the
genes studied, together with the location of their candidate binding
sites in the sequences. Pscan does not resort to comparisons with
orthologous sequences and experimental results show that it compares
favorably to other tools for the same task in terms of false positive
predictions and computation time. The website is free and open to all
users and there is no login requirement.
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psortb
bacterial localization prediction tool
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Versions of package psortb |
Release | Version | Architectures |
bullseye | 3.0.6+dfsg-2 | amd64 |
buster | 3.0.6+dfsg-1 | amd64 |
stretch-backports | 3.0.6+dfsg-1~bpo9+1 | amd64 |
sid | 3.0.6+dfsg-4 | amd64 |
trixie | 3.0.6+dfsg-4 | amd64 |
bookworm | 3.0.6+dfsg-3 | amd64 |
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License: DFSG free
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PSORTb enables prediction of bacterial protein subcellular localization
(SCL) and provides a quick and inexpensive means for gaining insight
into protein function, verifying experimental results, annotating newly
sequenced bacterial genomes, detecting potential cell surface/secreted
drug targets, as well as identifying biomarkers for microbes.
Please cite:
Nancy Y. Yu, James R. Wagner, Matthew R. Laird, Gabor Melli, Sébastien Rey, Raymond Lo, Phuong Dao, S. Cenk Sahinalp, Martin Ester, Leonard J. Foster and F. S. Brinkman:
PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes.
(PubMed,eprint)
Bioinformatics
26(13):1608-1615
(2010)
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pullseq
Extract sequence from a fasta or fastq
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Versions of package pullseq |
Release | Version | Architectures |
bookworm | 1.0.2-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.0.2-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.0.2-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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This is a utility to extract sequence from a fasta
or fastq. Also helps filter sequences by a minimum
length or maximum length. Fast, written in C, using
kseq.h library.
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pycoqc
computes metrics and generates Interactive QC plots
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Versions of package pycoqc |
Release | Version | Architectures |
bookworm | 2.5.2+dfsg-3 | all |
bullseye | 2.5.2+dfsg-1 | all |
sid | 2.5.2+dfsg-3 | all |
trixie | 2.5.2+dfsg-3 | all |
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License: DFSG free
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PycoQC computes metrics and generates interactive QC plots for Oxford
Nanopore technologies sequencing data
PycoQC relies on the sequencing_summary.txt file generated by Albacore
and Guppy, but if needed it can also generates a summary file from
basecalled fast5 files. The package supports 1D and 1D2 runs generated
with Minion, Gridion and Promethion devices and basecalled with Albacore
1.2.1+ or Guppy 2.1.3+
The package is enhanced by the following packages:
multiqc
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pycorrfit
tool for fitting correlation curves on a logarithmic plot
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Versions of package pycorrfit |
Release | Version | Architectures |
jessie | 0.8.3-2 | all |
trixie | 1.1.7+nopack-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.1.7+nopack-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.1.7+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.1.7+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.1.5+dfsg-1 | amd64,arm64,armhf,i386 |
stretch | 0.9.9+dfsg-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package pycorrfit: |
field | biology, mathematics, physics |
interface | x11 |
role | program |
science | modelling, plotting, visualisation |
scope | application |
uitoolkit | wxwidgets |
use | analysing, learning, organizing, viewing |
x11 | application |
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License: DFSG free
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PyCorrFit is a general-purpose FCS evaluation software that,
amongst other formats, supports the established Zeiss ConfoCor3 ~.fcs
file format. PyCorrFit comes with several built-in model functions,
covering a wide range of applications in standard confocal FCS.
In addition, it contains equations dealing with different excitation
geometries like total internal reflection (TIR).
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pyensembl
installs data from the Ensembl genome database
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Versions of package pyensembl |
Release | Version | Architectures |
trixie | 2.3.13-1 | all |
bookworm | 2.2.4+ds-1 | all |
sid | 2.3.13-1 | all |
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License: DFSG free
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The Ensembl genome database is an established reference
for genomic sequences and their automated annotation.
To have this data local has advantages for bulk analyses,
e.g. for the mapping of reads from RNA-seq against the
latest golden path - or a previous one to compare analyses.
This package provides a reproducible way to insatll this
data and thus simplify the automation of respective
workflows.
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pyfastx
fast random access to sequences from FASTA/Q file - command
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Versions of package pyfastx |
Release | Version | Architectures |
trixie | 2.1.0-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.1.0-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.8.4-2 | amd64,arm64,i386,mips64el,ppc64el,s390x |
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License: DFSG free
|
The pyfastx is a lightweight Python C extension that enables users to randomly
access to sequences from plain and gzipped FASTA/Q files. This module aims to
provide simple APIs for users to extract sequence from FASTA and reads from
FASTQ by identifier and index number. The pyfastx will build indexes stored in
a sqlite3 database file for random access to avoid consuming excessive amount
of memory. In addition, the pyfastx can parse standard (sequence is spread
into multiple lines with same length) and nonstandard (sequence is spread into
one or more lines with different length) FASTA format.
It features:
- a single file for the Python extension;
- lightweight, memory efficient FASTA/Q file parsing;
- fast random access to sequences from gzipped FASTA/Q file;
- sequences reading from FASTA file line by line;
- N50 and L50 calculation of sequences in FASTA file;
- GC content and nucleotides composition calculation;
- reverse, complement and antisense sequences extraction;
- excellent compatibility: support for parsing nonstandard FASTA file;
- support for FASTQ quality score conversion;
- a command line interface for splitting FASTA/Q file.
This package provides the command line interface.
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pymol
Molecular Graphics System
|
Versions of package pymol |
Release | Version | Architectures |
trixie | 3.0.0+dfsg-1 | all |
sid | 3.0.0+dfsg-1 | all |
bullseye | 2.4.0+dfsg-2 | all |
stretch | 1.8.4.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.5.0+dfsg-1 | all |
buster | 2.2.0+dfsg-4 | all |
jessie | 1.7.2.1-1 | amd64,armel,armhf,i386 |
Debtags of package pymol: |
field | biology:structural, chemistry |
interface | 3d, x11 |
role | program |
scope | utility |
uitoolkit | tk |
use | learning, viewing |
works-with | image |
x11 | application |
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License: DFSG free
|
PyMOL is a molecular graphics system targeted at medium to large
biomolecules like proteins. It can generate high-quality publication-ready
molecular graphics images and animations.
Features include:
- Visualization of molecules, molecular trajectories and surfaces
of crystallography data or orbitals
- Molecular builder and sculptor
- Internal raytracer and movie generator
- Fully extensible and scriptable via a Python interface
File formats PyMOL can read include PDB, XYZ, CIF, MDL Molfile, ChemDraw,
CCP4 maps, XPLOR maps and Gaussian cube maps.
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pyscanfcs
scientific tool for perpendicular line scanning FCS
|
Versions of package pyscanfcs |
Release | Version | Architectures |
trixie | 0.3.6+ds-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 0.2.2-2 | amd64,armel,armhf,i386 |
stretch | 0.2.3-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.3.6+ds-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.3.6+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.3.6+ds-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 0.3.2+ds-2 | amd64,arm64,armhf,i386 |
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License: DFSG free
|
When a membrane is scanned perpendicularly to its surface,
the fluorescence signal originating from the membrane itself
must be separated from the signal of the surrounding medium for
an FCS analysis. PyScanFCS interactively extracts the fluctuating
fluorescence signal from such measurements and applies a multiple-tau
algorithm. The obtained correlation curves can be evaluated using PyCorrFit.
Package provides the Python module pyscanfcs and its graphical user interface.
The graphical user interface is written in wxPython.
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python3-biomaj3-daemon
|
Versions of package python3-biomaj3-daemon |
Release | Version | Architectures |
bookworm | 3.0.24-2 | all |
trixie | 3.0.24-3 | all |
bullseye | 3.0.22-2 | all |
sid | 3.0.24-3 | all |
buster | 3.0.17-1 | all |
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License: DFSG free
|
BioMAJ downloads remote data banks, checks their status and applies
transformation workflows, with consistent state, to provide ready-to-use
data for biologists and bioinformaticians. For example, it can transform
original FASTA files into BLAST indexes. It is very flexible and its
post-processing facilities can be extended very easily.
BioMAJ3 is a rewrite of BioMAJ v1.x, see online documentation for migration.
This package contains the library and microservice to manage daemon and CLI
in BioMAJ3
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python3-bioxtasraw
process biological small angle scattering data
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Versions of package python3-bioxtasraw |
Release | Version | Architectures |
bookworm | 2.1.1-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
sid | 2.3.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
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License: DFSG free
|
BioXTAS RAW is a GUI based, Python program for reduction and
analysis of small-angle X-ray solution scattering (SAXS) data.
The package is designed for biological SAXS data.
BioXTAS RAW provides an alternative to closed source programs
such as Primus and Scatter for primary data analysis. Because
it can calibrate, mask, and integrate images it also provides
an alternative to synchrotron beamline pipelines that scientists
can install on their own computers and use both at home and at
the beamline.
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python3-cogent3
framework for genomic biology
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Versions of package python3-cogent3 |
Release | Version | Architectures |
bookworm | 2023.2.12a1+dfsg-2+deb12u1 | amd64,arm64,mips64el,ppc64el,s390x |
bullseye | 2020.12.21a+dfsg-4+deb11u1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2024.5.7a1+dfsg-3 | amd64,arm64,mips64el,ppc64el |
sid | 2023.12.15a1+dfsg-1 | s390x |
upstream | 2024.12.19a1 |
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License: DFSG free
|
PyCogent is a software library for genomic biology. It is a fully
integrated and thoroughly tested framework for:
- controlling third-party applications,
- devising workflows; querying databases,
- conducting novel probabilistic analyses of biological sequence
evolution, and
- generating publication quality graphics.
It is distinguished by many unique built-in capabilities (such as true codon
alignment) and the frequent addition of entirely new methods for the analysis
of genomic data.
Please cite:
Rob Knight, Peter Maxwell, Amanda Birmingham, Jason Carnes, J Gregory Caporaso, Brett C Easton, Michael Eaton, Micah Hamady, Helen Lindsay, Zongzhi Liu, Catherine Lozupone, Daniel McDonald, Michael Robeson, Raymond Sammut, Sandra Smit, Matthew J Wakefield, Jeremy Widmann, Shandy Wikman, Stephanie Wilson, Hua Ying and Gavin A Huttley:
PyCogent: a toolkit for making sense from sequence.
(PubMed,eprint)
Genome Biology
8(8):R171
(2007)
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python3-emperor
visualizing high-throughput microbial community data
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Versions of package python3-emperor |
Release | Version | Architectures |
bookworm | 1.0.3+ds-7 | all |
sid | 1.0.3+ds-9.1 | all |
trixie | 1.0.3+ds-9.1 | all |
upstream | 1.0.4 |
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License: DFSG free
|
Emperor is an interactive next generation tool for the analysis,
visualization and understanding of high throughput microbial
ecology datasets.
Due to its tailor-made graphical user interface, delving into a new
dataset to elucidate the patterns hidden in the data, has never been
easier. Emperor brings a rich set of customizations and modifications
that can be integrated into any QIIME or scikit-bio compliant dataset;
with lightweight data files and hardware accelerated graphics,
constitutes itself as the state of the art for analyzing N-dimensional
data using principal coordinates analysis.
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python3-geneimpacts
wraps command line tools to assess variants in gene sequences
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Versions of package python3-geneimpacts |
Release | Version | Architectures |
sid | 0.3.7-5 | all |
bullseye | 0.3.7-3 | all |
bookworm | 0.3.7-4 | all |
trixie | 0.3.7-5 | all |
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License: DFSG free
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Interpersonal differences in DNA is responsible for variations in
response to external stimuli, the efficiency of metabolism or
may even cause what is referenced as a genetic disorder.
A range of tools have been created to predict the importance of
differences (polymorphisms) in genetic sequences at single nucleotides,
SNPs. This Python class wraps and represents findings provided by any
of the tools snpEff, VEP and BCFT.
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python3-gffutils
Work with GFF and GTF files in a flexible database framework
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Versions of package python3-gffutils |
Release | Version | Architectures |
bookworm | 0.11.1-3 | all |
trixie | 0.13-1 | all |
bullseye | 0.10.1-2 | all |
sid | 0.13-1 | all |
buster | 0.9-1 | all |
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License: DFSG free
|
A Python package for working with and manipulating the GFF and GTF format
files typically used for genomic annotations. Files are loaded into a
sqlite3 database, allowing much more complex manipulation of hierarchical
features (e.g., genes, transcripts, and exons) than is possible with
plain-text methods alone.
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python3-pairtools
Framework to process sequencing data from a Hi-C experiment
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Versions of package python3-pairtools |
Release | Version | Architectures |
trixie | 1.1.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
bookworm | 1.0.2-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
bullseye | 0.3.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.1.2-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
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License: DFSG free
|
Simple and fast command-line framework to process sequencing data from a Hi-C
experiment.
Process pair-end sequence alignments and perform the following operations:
- Detect ligation junctions (a.k.a. Hi-C pairs) in aligned paired-end
sequences of Hi-C DNA molecules
- Sort .pairs files for downstream analyses
- Detect, tag and remove PCR/optical duplicates
- Generate extensive statistics of Hi-C datasets
- Select Hi-C pairs given flexibly defined criteria
- Restore .sam alignments from Hi-C pairs
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python3-pybedtools
Python 3 wrapper around BEDTools for bioinformatics work
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Versions of package python3-pybedtools |
Release | Version | Architectures |
bullseye | 0.8.0-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
sid | 0.10.0-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
buster | 0.8.0-1 | amd64,arm64 |
trixie | 0.10.0-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
bookworm | 0.9.0-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
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License: DFSG free
|
The BEDTools suite of programs is widely used for genomic interval
manipulation or “genome algebra”. pybedtools wraps and extends BEDTools and
offers feature-level manipulations from within Python.
This is the Python 3 version.
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python3-sqt
SeQuencing Tools for biological DNA/RNA high-throughput data
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Versions of package python3-sqt |
Release | Version | Architectures |
sid | 0.8.0-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
bullseye | 0.8.0-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
buster | 0.8.0-3 | amd64,arm64 |
trixie | 0.8.0-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
bookworm | 0.8.0-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
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License: DFSG free
|
sqt is a collection of command-line tools for working with
high-throughput sequencing data. Conceptionally not fixed to use any
particular language, many sqt subcommands are currently implemented
in Python. For them, a Python package is available with functions for
reading and writing FASTA/FASTQ files, computing alignments, quality
trimming, etc.
The following tools are offered:
- sqt-coverage -- Compute per-reference statistics such as coverage
and GC content
- sqt-fastqmod -- FASTQ modifications: shorten, subset, reverse
complement, quality trimming.
- sqt-fastastats -- Compute N50, min/max length, GC content etc. of
a FASTA file
- sqt-qualityguess -- Guess quality encoding of one or more FASTA files.
- sqt-globalalign -- Compute a global or semiglobal alignment of two strings.
- sqt-chars -- Count length of the first word given on the command line.
- sqt-sam-cscq -- Add the CS and CQ tags to a SAM file with colorspace reads.
- sqt-fastamutate -- Add substitutions and indels to sequences in a
FASTA file.
- sqt-fastaextract -- Efficiently extract one or more regions from an
indexed FASTA file.
- sqt-translate -- Replace characters in FASTA files (like the 'tr'
command).
- sqt-sam-fixn -- Replace all non-ACGT characters within reads in a
SAM file.
- sqt-sam-insertsize -- Mean and standard deviation of paired-end
insert sizes.
- sqt-sam-set-op -- Set operations (union, intersection, ...) on
SAM/BAM files.
- sqt-bam-eof -- Check for the End-Of-File marker in compressed
BAM files.
- sqt-checkfastqpe -- Check whether two FASTQ files contain correctly
paired paired-end data.
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python3-treetime
inference of time stamped phylogenies and ancestral reconstruction (Python 3)
|
Versions of package python3-treetime |
Release | Version | Architectures |
trixie | 0.11.4-1 | all |
bookworm | 0.9.4-1 | all |
bullseye | 0.8.1-1 | all |
buster | 0.5.3-1 | all |
sid | 0.11.4-1 | all |
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License: DFSG free
|
TreeTime provides routines for ancestral sequence reconstruction and the
maximum likelihoo inference of molecular-clock phylogenies, i.e., a tree
where all branches are scaled such that the locations of terminal nodes
correspond to their sampling times and internal nodes are placed at the
most likely time of divergence.
TreeTime aims at striking a compromise between sophisticated
probabilistic models of evolution and fast heuristics. It implements GTR
models of ancestral inference and branch length optimization, but takes
the tree topology as given. To optimize the likelihood of time-scaled
phylogenies, treetime uses an iterative approach that first infers
ancestral sequences given the branch length of the tree, then optimizes
the positions of unconstraine d nodes on the time axis, and then repeats
this cycle. The only topology optimization are (optional) resolution of
polytomies in a way that is most (approximately) consistent with the
sampling time constraints on the tree. The package is designed to be
used as a stand-alone tool or as a library used in larger phylogenetic
analysis workflows.
Features
- ancestral sequence reconstruction (marginal and joint maximum
likelihood)
- molecular clock tree inference (marginal and joint maximum
likelihood)
- inference of GTR models
- rerooting to obtain best root-to-tip regression
- auto-correlated relaxed molecular clock (with normal prior)
This package provides the Python 3 module.
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pyvcf
helper scripts for Variant Call Format (VCF) parser
|
Versions of package pyvcf |
Release | Version | Architectures |
buster | 0.6.8+git20170215.476169c-1 | all |
bullseye | 0.6.8+git20170215.476169c-7 | all |
bookworm | 0.6.8+git20170215.476169c-9 | all |
sid | 0.6.8+git20170215.476169c-11 | all |
trixie | 0.6.8+git20170215.476169c-11 | all |
stretch | 0.6.8-1 | all |
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License: DFSG free
|
The Variant Call Format (VCF) specifies the format of a text file used
in bioinformatics for storing gene sequence variations. The format has
been developed with the advent of large-scale genotyping and DNA
sequencing projects, such as the 1000 Genomes Project.
The intent of this module is to mimic the csv module in the Python
stdlib, as opposed to more flexible serialization formats like JSON or
YAML. vcf will attempt to parse the content of each record based on
the data types specified in the meta-information lines -- specifically
the ##INFO and
##FORMAT lines. If these lines are missing or incomplete, it will check
against the reserved types mentioned in the spec. Failing that, it will
just return strings.
This package provides helper scripts using python3-pyvcf.
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qcat
demultiplexing Oxford Nanopore reads from FASTQ files
|
Versions of package qcat |
Release | Version | Architectures |
sid | 1.1.0-7 | all |
bullseye | 1.1.0-2 | all |
bookworm | 1.1.0-6 | all |
trixie | 1.1.0-7 | all |
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License: DFSG free
|
Qcat is a command-line tool for demultiplexing Oxford Nanopore reads
from FASTQ files. It accepts basecalled FASTQ files and splits the reads
into separate FASTQ files based on their barcode. Qcat makes the
demultiplexing algorithms used in albacore/guppy and EPI2ME available to
be used locally with FASTQ files. Currently qcat implements the EPI2ME
algorithm.
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qcumber
quality control of genomic sequences
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Versions of package qcumber |
Release | Version | Architectures |
bullseye | 2.3.0-2 | all |
buster | 1.0.14+dfsg-1 | all |
sid | 2.3.0-2 | all |
trixie | 2.3.0-2 | all |
bookworm | 2.3.0-2 | all |
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License: DFSG free
|
QCPipeline is a tool for quality control. The workflow is as follows:
1. Quality control with FastQC
2. Trim Reads with Trimmomatic
3. Quality control of trimmed reads with FastQC
4. Map reads against reference using bowtie2
5. Classify reads with Kraken
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qiime
Quantitative Insights Into Microbial Ecology
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Versions of package qiime |
Release | Version | Architectures |
bullseye | 2020.11.1-1 | all |
jessie | 1.8.0+dfsg-4 | amd64,armel,armhf,i386 |
sid | 2024.5.0-1 | all |
bookworm | 2022.11.1-2 | all |
upstream | 2024.10.1 |
Debtags of package qiime: |
role | program |
|
License: DFSG free
|
Microbes are surrounding us, animals, plants and all their parasites with
strong effect on these and the environment these live in. Soil quality comes
to mind but also the effect that bacteria have on each other. Humans are
influencing the absolute and relative abundance of bacteria by antibiotics,
food, fertilizers - you name it - and these changes affect us.
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
researchers to start an analysis with raw DNA sequence data and finish with
publication-quality figures and statistical results.
Key features:
- Integrated and automatic tracking of data provenance
- Semantic type system
- Plugin system for extending microbiome analysis functionality
- Support for multiple types of user interfaces (e.g. API, command line,
graphical)
QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis
pipeline. QIIME 2 will address many of the limitations of QIIME 1, while
retaining the features that makes QIIME 1 a powerful and widely-used analysis
pipeline.
QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline.
New functionality will regularly become available through QIIME 2 plugins. You
can view a list of plugins that are currently available on the QIIME 2 plugin
availability page. The future plugins page lists plugins that are being
developed.
Please cite:
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso:
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
(PubMed,eprint)
Nature Biotechnology
37:852 - 857
(2019)
Topics: Microbial ecology
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qtltools
Tool set for molecular QTL discovery and analysis
|
Versions of package qtltools |
Release | Version | Architectures |
sid | 1.3.1+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.1+dfsg-3 | amd64,arm64,armhf |
stretch | 1.1+dfsg-1 | amd64,arm64,armel,i386,mips64el,mipsel,ppc64el |
bullseye | 1.3.1+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.3.1+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.3.1+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
QTLtools is a tool set for molecular Quantitative Trait Loci (QTL) discovery
and analysis. It allows user to go from the raw sequence data to collection of
molecular QTL in few easy-to-perform steps. QTLtools contains multiple methods
to prepare the data, to discover proximal and distal molecular QTL and to
finally integrate them with GWAS variants and functional annotations of the
genome.
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quicktree
Neighbor-Joining algorithm for phylogenies
|
Versions of package quicktree |
Release | Version | Architectures |
sid | 2.5-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 2.5-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.5-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.5-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
|
QuickTree is an efficient implementation of the Neighbor-Joining
algorithm (PMID: 3447015), capable of reconstructing phylogenies from
huge alignments in time less than the age of the universe.
QuickTree accepts both distance matrix and multiple-sequence-aligment
inputs. The former should be in PHYLIP format. The latter should be
in Stockholm format, which is the native alignment format for the Pfam
database. Alignments in various formats can be converted to Stockholm
format with the sreformat program, which is part of the HMMer package
(hmmer.org).
The tress are written to stdout, in the Newick/New-Hampshire format
use by PHYLIP and many other programs
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quorum
QUality Optimized Reads of genomic sequences
|
Versions of package quorum |
Release | Version | Architectures |
bookworm | 1.1.1-7 | amd64,arm64,mips64el,ppc64el |
buster | 1.1.1-2 | amd64,arm64 |
bullseye | 1.1.1-4 | amd64,arm64,mips64el,ppc64el |
sid | 1.1.2-2 | amd64,arm64,mips64el,ppc64el,riscv64 |
trixie | 1.1.2-2 | amd64,arm64,mips64el,ppc64el,riscv64 |
|
License: DFSG free
|
QuorUM enables to obtain trimmed and error-corrected reads that result
in assemblies with longer contigs and fewer errors. QuorUM provides best
performance compared to other published error correctors in several
metrics. QuorUM is efficiently implemented making use of current multi-
core computing architectures and it is suitable for large data sets (1
billion bases checked and corrected per day per core). The third-party
assembler (SOAPdenovo) benefits significantly from using QuorUM error-
corrected reads. QuorUM error corrected reads result in a factor of 1.1
to 4 improvement in N50 contig size compared to using the original reads
with SOAPdenovo for the data sets investigated.
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qutemol
interactive visualization of macromolecules
|
Versions of package qutemol |
Release | Version | Architectures |
stretch | 0.4.1~cvs20081111-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0.4.1~cvs20081111-3.2 | amd64,armel,armhf,i386 |
buster | 0.4.1~cvs20081111-12 | amd64,arm64,armhf,i386 |
bullseye | 0.4.1~cvs20081111-13 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.4.1~cvs20081111-15 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.4.1~cvs20081111-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.4.1~cvs20081111-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package qutemol: |
interface | x11 |
role | program |
uitoolkit | glut, wxwidgets |
x11 | application |
|
License: DFSG free
|
QuteMol is an interactive, high quality molecular visualization
system. It exploits the current GPU capabilities through OpenGL shaders
to offer an array of innovative visual effects. QuteMol visualization
techniques are aimed at improving clarity and an easier understanding
of the 3D shape and structure of large molecules or complex proteins.
Qutemol uses advanced OpenGL techniques and might not work correctly
with all video cards and drivers.
Features QuteMol offers include:
- Real time ambient occlusion
- Depth aware silhouette enhancement
- Ball-and-stick, space-filling and liquorice visualization modes
- High resolution antialiased snapshots for creating publication
quality renderings
- Automatic generation of animated gifs of rotating molecules for
web page animations
- Interactive rendering of macromolecules (>100k atoms)
QuteMol reads PDB files as input.
|
|
r-bioc-annotate
BioConductor annotation for microarrays
|
Versions of package r-bioc-annotate |
Release | Version | Architectures |
bullseye | 1.68.0+dfsg-1 | all |
buster | 1.60.0+dfsg-1 | all |
experimental | 1.84.0+dfsg-1 | all |
trixie | 1.82.0+dfsg-1 | all |
bookworm | 1.76.0+dfsg-1 | all |
stretch | 1.52.1+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.82.0+dfsg-1 | all |
upstream | 1.84.0 |
|
License: DFSG free
|
This BioConductor module provides methods for annotation for microarrays.
In its current state the basic purpose of annotate is to
supply interface routines that support user actions that rely on the
different meta-data packages provided through the Bioconductor
Project.
|
|
r-bioc-biostrings
GNU R string objects representing biological sequences
|
Versions of package r-bioc-biostrings |
Release | Version | Architectures |
jessie | 2.32.1-1 | amd64,armel,armhf,i386 |
experimental | 2.74.0+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
stretch | 2.42.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.50.2-1 | amd64,arm64,armhf,i386 |
bullseye | 2.58.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.72.1+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.66.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.72.1+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
upstream | 2.74.1 |
|
License: DFSG free
|
Memory efficient string containers, string matching algorithms, and other
utilities, for fast manipulation of large biological sequences or set of
sequences.
|
|
r-bioc-bitseq
transcript expression inference and analysis for RNA-seq data
|
Versions of package r-bioc-bitseq |
Release | Version | Architectures |
bullseye | 1.34.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.26.1+dfsg-1 | amd64,arm64,armhf,i386 |
|
License: DFSG free
|
The BitSeq package is targeted for transcript expression
analysis and differential expression analysis of RNA-seq data
in two stage process. In the first stage it uses Bayesian
inference methodology to infer expression of individual
transcripts from individual RNA-seq experiments. The second
stage of BitSeq embraces the differential expression analysis
of transcript expression. Providing expression estimates from
replicates of multiple conditions, Log-Normal model of the
estimates is used for inferring the condition mean transcript
expression and ranking the transcripts based on the likelihood
of differential expression.
|
|
r-bioc-cner
CNE Detection and Visualization
|
Versions of package r-bioc-cner |
Release | Version | Architectures |
sid | 1.40.0+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.26.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
experimental | 1.42.0+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.34.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.40.0+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
buster | 1.18.1+dfsg-1 | amd64,arm64,armhf,i386 |
upstream | 1.42.0 |
|
License: DFSG free
|
Large-scale identification and advanced visualization
of sets of conserved noncoding elements.
|
|
r-bioc-cummerbund
tool for analysis of Cufflinks RNA-Seq output
|
Versions of package r-bioc-cummerbund |
Release | Version | Architectures |
sid | 2.46.0-1 | all |
bookworm | 2.40.0-1 | all |
bullseye | 2.32.0-1 | all |
jessie | 2.6.1-1 | all |
stretch | 2.16.0-2 | all |
trixie | 2.46.0-1 | all |
buster | 2.24.0-2 | all |
experimental | 2.48.0-1 | all |
upstream | 2.48.0 |
|
License: DFSG free
|
Allows for persistent storage, access, exploration, and manipulation of
Cufflinks high-throughput sequencing data. In addition, provides
numerous plotting functions for commonly used visualizations.
Please cite:
L. Goff and C. Trapnell:
cummeRbund: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data
(2012)
|
|
r-bioc-deseq2
R package for RNA-Seq Differential Expression Analysis
|
Versions of package r-bioc-deseq2 |
Release | Version | Architectures |
stretch | 1.14.1-1 | amd64,arm64,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 1.44.0+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
sid | 1.44.0+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
buster | 1.22.2+dfsg-1 | amd64,arm64,armhf,i386 |
experimental | 1.46.0+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.30.1+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.38.3+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 1.46.0 |
|
License: DFSG free
|
Differential gene expression analysis based on the negative binomial
distribution. Estimate variance-mean dependence in count data from
high-throughput sequencing assays and test for differential expression based
on a model using the negative binomial distribution.
|
|
r-bioc-ebseq
R package for RNA-Seq Differential Expression Analysis
|
Versions of package r-bioc-ebseq |
Release | Version | Architectures |
bookworm | 1.38.0-1 | all |
stretch | 1.14.0-1 | all |
buster | 1.22.1-2 | all |
sid | 2.2.0-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
trixie | 2.2.0-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
experimental | 2.4.0-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.30.0-1 | all |
upstream | 2.4.0 |
|
License: DFSG free
|
r-bioc-ebseq is an R package for identifying genes and isoforms differentially
expressed (DE) across two or more biological conditions in an RNA-seq
experiment.
|
|
r-bioc-edger
Empirical analysis of digital gene expression data in R
|
Versions of package r-bioc-edger |
Release | Version | Architectures |
trixie | 4.2.2+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bookworm | 3.40.2+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
experimental | 4.4.1+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
sid | 4.2.2+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bullseye | 3.32.1+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 3.8.2+dfsg-1 | amd64,armel,armhf,i386 |
stretch | 3.14.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
upstream | 4.4.1 |
|
License: DFSG free
|
Bioconductor package for differential expression analysis of whole
transcriptome sequencing (RNA-seq) and digital gene expression
profiles with biological replication. It uses empirical Bayes
estimation and exact tests based on the negative binomial
distribution. It is also useful for differential signal analysis with
other types of genome-scale count data.
|
|
r-bioc-genefilter
methods for filtering genes from microarray experiments
|
Versions of package r-bioc-genefilter |
Release | Version | Architectures |
buster | 1.64.0-1 | amd64,arm64,armhf,i386 |
trixie | 1.86.0-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
sid | 1.86.0-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.72.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
experimental | 1.88.0-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
stretch | 1.56.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.80.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 1.88.0 |
|
License: DFSG free
|
This BioConductor module provides methods for filtering genes from microarray
experiments. It contains some basic functions for filtering genes.
|
|
r-bioc-geoquery
Get data from NCBI Gene Expression Omnibus (GEO)
|
Versions of package r-bioc-geoquery |
Release | Version | Architectures |
bookworm | 2.66.0+dfsg-1 | all |
bullseye | 2.58.0+dfsg-2 | all |
trixie | 2.72.0+dfsg-1 | all |
sid | 2.72.0+dfsg-1 | all |
experimental | 2.74.0+dfsg-1 | all |
upstream | 2.74.0 |
|
License: DFSG free
|
The NCBI Gene Expression Omnibus (GEO) is a public repository of
microarray data. Given the rich and varied nature of this resource, it
is only natural to want to apply BioConductor tools to these data.
GEOquery is the bridge between GEO and BioConductor.
Please cite:
Sean Davis and Paul Meltzer:
GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor
Bioinformatics
14,:1846-1847,
(2007,)
|
|
r-bioc-hilbertvis
GNU R package to visualise long vector data
|
Versions of package r-bioc-hilbertvis |
Release | Version | Architectures |
bullseye | 1.48.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.62.0-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
experimental | 1.64.0-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.56.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.32.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.24.0-1 | amd64,armel,armhf,i386 |
sid | 1.62.0-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
buster | 1.40.0-1 | amd64,arm64,armhf,i386 |
upstream | 1.64.0 |
Debtags of package r-bioc-hilbertvis: |
biology | nuceleic-acids |
field | biology, biology:bioinformatics |
use | analysing |
|
License: DFSG free
|
This tool allows one to display very long data vectors in a space-efficient
manner, by organising it along a 2D Hilbert curve. The user can then
visually judge the large scale structure and distribution of features
simultaenously with the rough shape and intensity of individual features.
In bioinformatics, a typical use case is ChIP-Chip and ChIP-Seq,
or basically all the kinds of genomic data, that are conventionally
displayed as quantitative track ("wiggle data") in genome browsers such
as those provided by Ensembl or UCSC.
|
|
r-bioc-htsfilter
GNU R filter replicated high-throughput transcriptome sequencing data
|
Versions of package r-bioc-htsfilter |
Release | Version | Architectures |
trixie | 1.44.0+dfsg-1 | all |
experimental | 1.46.0+dfsg-1 | all |
bullseye | 1.30.1+dfsg-1 | all |
bookworm | 1.38.0+dfsg-2 | all |
sid | 1.44.0+dfsg-1 | all |
upstream | 1.46.0 |
|
License: DFSG free
|
This package implements a filtering procedure for
replicated transcriptome sequencing data based on a global
Jaccard similarity index in order to identify genes with low,
constant levels of expression across one or more experimental
conditions.
|
|
r-bioc-impute
Imputation for microarray data
|
Versions of package r-bioc-impute |
Release | Version | Architectures |
bullseye | 1.64.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.78.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.72.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.78.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
experimental | 1.80.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.56.0-1 | amd64,arm64,armhf,i386 |
upstream | 1.80.0 |
|
License: DFSG free
|
R package which provide a function to perform imputation for
microarray data (currently KNN only).
|
|
r-bioc-limma
linear models for microarray data
|
Versions of package r-bioc-limma |
Release | Version | Architectures |
experimental | 3.62.1+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bookworm | 3.54.1+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 3.60.6+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
trixie | 3.60.6+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bullseye | 3.46.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 3.22.1+dfsg-1 | amd64,armel,armhf,i386 |
buster | 3.38.3+dfsg-1 | amd64,arm64,armhf,i386 |
stretch | 3.30.8+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
upstream | 3.62.1 |
|
License: DFSG free
|
Microarrays are microscopic plates with carefully arranged short DNA
strands and/or chemically prepared surfaces to which other DNA
preferably binds. The amount of DNA binding at different locations of
these chips, typically determined by a fluorescent dye, is to be
interpreted. The technology is typically used with DNA that is derived
from RNA, i.e to determine the activity of a gene and/or its splice
variants. But the technology is also used to determine sequence
variations in genomic DNA.
This Bioconductor package supports the analysis of gene expression
microarray data, especially the use of linear models for analysing
designed experiments and the assessment of differential expression. The
package includes pre-processing capabilities for two-colour spotted
arrays. The differential expression methods apply to all array platforms
and treat Affymetrix, single channel and two channel experiments in a
unified way.
|
|
r-bioc-megadepth
BioCOnductor BigWig and BAM related utilities
|
Versions of package r-bioc-megadepth |
Release | Version | Architectures |
bookworm | 1.8.0+ds-1 | all |
experimental | 1.16.0+ds-1 | all |
sid | 1.14.0+ds-1 | all |
upstream | 1.16.0 |
|
License: DFSG free
|
This package provides an R interface to Megadepth by Christopher
Wilks available at https://github.com/ChristopherWilks/megadepth. It is
particularly useful for computing the coverage of a set of genomic regions
across bigWig or BAM files. With this package, you can build base-pair
coverage matrices for regions or annotations of your choice from BigWig
files. Megadepth was used to create the raw files provided by
https://bioconductor.org/packages/recount3.
|
|
r-bioc-mergeomics
Integrative network analysis of omics data
|
Versions of package r-bioc-mergeomics |
Release | Version | Architectures |
bookworm | 1.26.0-1 | all |
stretch | 1.2.0-1 | all |
trixie | 1.32.0-1 | all |
bullseye | 1.18.0-1 | all |
experimental | 1.34.0-1 | all |
buster | 1.10.0-1 | all |
sid | 1.32.0-1 | all |
upstream | 1.34.0 |
|
License: DFSG free
|
The Mergeomics pipeline serves as a flexible framework for integrating
multidimensional omics-disease associations, functional genomics,
canonical pathways and gene-gene interaction networks to generate
mechanistic hypotheses. It includes two main parts:
1) Marker set enrichment analysis (MSEA);
2) Weighted Key Driver Analysis (wKDA).
Please cite:
Le Shu, Yuqi Zhao, Zeyneb Kurt, Sean Geoffrey Byars, Taru Tukiainen, Johannes Kettunen, Luz D. Orozco, Matteo Pellegrini, Aldons J. Lusis, Samuli Ripatti, Bin Zhang, Michael Inouye, Ville-Petteri Mäkinen and Xia Yang:
Mergeomics: multidimensional data integration to identify pathogenic perturbations to biological systems.
(eprint)
BMC Genomics
(2016)
|
|
r-bioc-metagenomeseq
GNU R statistical analysis for sparse high-throughput sequencing
|
Versions of package r-bioc-metagenomeseq |
Release | Version | Architectures |
experimental | 1.46.0-2 | all |
bullseye | 1.32.0-1 | all |
trixie | 1.46.0-1 | all |
sid | 1.46.0-1 | all |
stretch | 1.16.0-2 | all |
bookworm | 1.40.0-1 | all |
buster | 1.24.1-1 | all |
|
License: DFSG free
|
MetagenomeSeq is designed to determine features (be it Operational
Taxanomic Unit (OTU), species, etc.) that are differentially abundant
between two or more groups of multiple samples. metagenomeSeq is
designed to address the effects of both normalization and under-sampling
of microbial communities on disease association detection and the
testing of feature correlations.
|
|
r-bioc-mofa
Multi-Omics Factor Analysis (MOFA)
|
Versions of package r-bioc-mofa |
Release | Version | Architectures |
bookworm | 1.6.1+dfsg-10 | all |
experimental | 1.6.1+dfsg-14 | all |
sid | 1.6.1+dfsg-13 | all |
bullseye | 1.6.1+dfsg-1 | all |
|
License: DFSG free
|
Multi-Omics Factor Analysis: an unsupervised framework for the
integration of multi-omics data sets.
Upstream no longer supports this package. This package only still
ships to help with rerunning/comparing/transitioning existing projects.
For new projects please upgrade to MOFA2 (MOFA+). Actually, also when
adding new data to old projects, MOFA2 has further improved the handling
of multiple factors, and to compensate for a batch effect that is likely
introduced with additional data, may be an immediate use case for that
new version.
Please cite:
Ricard Argelaguet, Britta Velten, Damien Arnol, Sascha Dietrich, Thorsten Zenz, John C Marioni, Florian Buettner, Wolfgang Huber and Oliver Stegle:
Link
to publication
Mol Syst Biol
14:e8124
(2018)
|
|
r-bioc-multiassayexperiment
Software for integrating multi-omics experiments in BioConductor
|
Versions of package r-bioc-multiassayexperiment |
Release | Version | Architectures |
trixie | 1.30.3+dfsg-2 | all |
bullseye | 1.16.0+dfsg-1 | all |
bookworm | 1.24.0+dfsg-2 | all |
sid | 1.30.3+dfsg-2 | all |
experimental | 1.32.0+dfsg-1 | all |
upstream | 1.32.0 |
|
License: DFSG free
|
MultiAssayExperiment harmonizes data management of
multiple assays performed on an overlapping set of specimens. It provides a
familiar Bioconductor user experience by extending concepts from
SummarizedExperiment, supporting an open-ended mix of standard data classes
for individual assays, and allowing subsetting by genomic ranges or rownames.
|
|
r-bioc-mutationalpatterns
GNU R comprehensive genome-wide analysis of mutational processes
|
Versions of package r-bioc-mutationalpatterns |
Release | Version | Architectures |
trixie | 3.14.0+dfsg-1 | all |
experimental | 3.16.0+dfsg-1 | all |
sid | 3.14.0+dfsg-1 | all |
bullseye | 3.0.1+dfsg-2 | all |
bookworm | 3.8.1+dfsg-1 | all |
upstream | 3.16.0 |
|
License: DFSG free
|
This BioConductor package provides an extensive toolset for the
characterization and visualization of a wide range of mutational patterns
in base substitution catalogs.
|
|
r-bioc-phyloseq
GNU R handling and analysis of high-throughput microbiome census data
|
Versions of package r-bioc-phyloseq |
Release | Version | Architectures |
trixie | 1.48.0+dfsg-1 | all |
stretch | 1.19.1-2 | all |
experimental | 1.50.0+dfsg-1 | all |
bullseye | 1.34.0+dfsg-1 | all |
bookworm | 1.42.0+dfsg-1 | all |
buster | 1.26.1+dfsg-1 | all |
sid | 1.48.0+dfsg-1 | all |
upstream | 1.50.0 |
|
License: DFSG free
|
The Bioconductor module phyloseq provides a set of classes and tools to
facilitate the import, storage, analysis, and graphical display of
microbiome census data.
|
|
r-bioc-rtracklayer
GNU R interface to genome browsers and their annotation tracks
|
Versions of package r-bioc-rtracklayer |
Release | Version | Architectures |
experimental | 1.66.0-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.50.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.24.2-1 | amd64,armel,armhf,i386 |
sid | 1.64.0-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
stretch | 1.34.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.42.1-2 | amd64,arm64,armhf,i386 |
bookworm | 1.58.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.64.0-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
upstream | 1.66.0 |
|
License: DFSG free
|
Extensible framework for interacting with multiple genome browsers
(currently UCSC built-in) and manipulating annotation tracks in various
formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
built-in). The user may export/import tracks to/from the supported
browsers, as well as query and modify the browser state, such as the
current viewport.
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r-bioc-scater
Single-Cell Analysis Toolkit for Gene Expression Data in R
|
Versions of package r-bioc-scater |
Release | Version | Architectures |
sid | 1.32.1+ds-1 | all |
bullseye | 1.18.3+ds-4 | all |
bookworm | 1.26.1+ds-1 | all |
experimental | 1.34.0+ds-1 | all |
upstream | 1.34.0 |
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License: DFSG free
|
A collection of tools for doing various analyses of
single-cell RNA-seq gene expression data, with a focus on
quality control and visualization.
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r-bioc-tfbstools
GNU R Transcription Factor Binding Site (TFBS) Analysis
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Versions of package r-bioc-tfbstools |
Release | Version | Architectures |
experimental | 1.44.0+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
sid | 1.42.0+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
trixie | 1.42.0+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
buster | 1.20.0+dfsg-1 | amd64,arm64,armhf,i386 |
bullseye | 1.28.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.36.0+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 1.44.0 |
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License: DFSG free
|
TFBSTools is a package for the analysis and manipulation of
transcription factor binding sites. It includes matrices conversion
between Position Frequency Matirx (PFM), Position Weight Matirx (PWM)
and Information Content Matrix (ICM). It can also scan putative TFBS
from sequence/alignment, query JASPAR database and provides a wrapper of
de novo motif discovery software.
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r-cran-adegenet
GNU R exploratory analysis of genetic and genomic data
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Versions of package r-cran-adegenet |
Release | Version | Architectures |
trixie | 2.1.10-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 2.1.1-2 | amd64,arm64,armhf,i386 |
stretch | 2.0.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.1.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.1.10-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.1.10-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
Toolset for the exploration of genetic and genomic data. Adegenet
provides formal (S4) classes for storing and handling various genetic
data, including genetic markers with varying ploidy and hierarchical
population structure ('genind' class), alleles counts by populations
('genpop'), and genome-wide SNP data ('genlight'). It also implements
original multivariate methods (DAPC, sPCA), graphics, statistical tests,
simulation tools, distance and similarity measures, and several spatial
methods. A range of both empirical and simulated datasets is also
provided to illustrate various methods.
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r-cran-adephylo
GNU R exploratory analyses for the phylogenetic comparative method
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Versions of package r-cran-adephylo |
Release | Version | Architectures |
bookworm | 1.1-13-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.1-10-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.1-11-3 | amd64,arm64,armhf,i386 |
bullseye | 1.1-11-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.1-16-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.1-16-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
|
This GNU R package provides multivariate tools to analyze comparative
data, i.e. a phylogeny and some traits measured for each taxa.
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r-cran-alakazam
Immunoglobulin Clonal Lineage and Diversity Analysis
|
Versions of package r-cran-alakazam |
Release | Version | Architectures |
trixie | 1.3.0-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.2.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.1.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
experimental | 1.3.0-2~0exp0 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
buster | 0.2.11-1 | amd64,arm64,armhf,i386 |
sid | 1.3.0-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
Alakazam is part of the Immcantation analysis framework for Adaptive
Immune Receptor Repertoire sequencing (AIRR-seq) and provides a set of
tools to investigate lymphocyte receptor clonal lineages, diversity,
gene usage, and other repertoire level properties, with a focus on
high-throughput immunoglobulin (Ig) sequencing.
Alakazam serves five main purposes:
- Providing core functionality for other R packages in the Immcantation
framework. This includes common tasks such as file I/O, basic DNA
sequence manipulation, and interacting with V(D)J segment and gene
annotations.
- Providing an R interface for interacting with the output of the
pRESTO and Change-O tool suites.
- Performing lineage reconstruction on clonal populations of Ig
sequences and analyzing the topology of the resultant lineage trees.
- Performing clonal abundance and diversity analysis on lymphocyte
repertoires.
- Performing physicochemical property analyses of lymphocyte receptor
sequences.
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r-cran-ape
GNU R package for Analyses of Phylogenetics and Evolution
|
Versions of package r-cran-ape |
Release | Version | Architectures |
buster | 5.2-1 | amd64,arm64,armhf,i386 |
trixie | 5.8-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 5.8-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 5.7-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 3.1-4-1 | amd64,armel,armhf,i386 |
bullseye | 5.4-1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 4.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
upstream | 5.8-1 |
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License: DFSG free
|
This package provides functions for reading, writing, plotting, and
manipulating phylogenetic trees, analyses of comparative data in a
phylogenetic framework, ancestral character analyses, analyses of
diversification and macroevolution, computing distances from DNA
sequences, reading and writing nucleotide sequences as well as
importing from BioConductor, and several tools such as Mantel's test,
generalized skyline plots, graphical exploration of phylogenetic data
(alex, trex, kronoviz), estimation of absolute evolutionary rates and
clock-like trees using mean path lengths and penalized likelihood,
dating trees with non-contemporaneous sequences, translating DNA into
AA sequences, and assessing sequence alignments. Phylogeny estimation
can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods,
and several methods handling incomplete distance matrices (NJ,
BIONJ, MVR*, and the corresponding triangle method). Some functions
call external applications (PhyML, Clustal, T-Coffee, Muscle) whose
results are returned into R.
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r-cran-bio3d
GNU R package for biological structure analysis
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Versions of package r-cran-bio3d |
Release | Version | Architectures |
stretch | 2.3-1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 2.4-4-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.4-4-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.4-1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.3-4-2 | amd64,arm64,armhf,i386 |
sid | 2.4-4-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 2.4-5 |
|
License: DFSG free
|
The bio3d package contains utilities to process, organize and explore
protein structure, sequence and dynamics data. Features include the
ability to read and write structure, sequence and dynamic trajectory
data, perform atom summaries, atom selection, re-orientation,
superposition, rigid core identification, clustering, torsion analysis,
distance matrix analysis, structure and sequence conservation analysis,
and principal component analysis (PCA). In addition, various utility
functions are provided to enable the statistical and graphical power of
the R environment to work with biological sequence and structural data.
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r-cran-distory
GNU R distance between phylogenetic histories
|
Versions of package r-cran-distory |
Release | Version | Architectures |
bookworm | 1.4.4-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.4.4-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.4.3-2 | amd64,arm64,armhf,i386 |
stretch | 1.4.2-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.4.4-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.4.4-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 1.4.5 |
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License: DFSG free
|
This GNU R package enables calculation of geodesic distance between
phylogenetic trees and associated functions.
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r-cran-genabel
GNU R package for genome-wide SNP association analysis
|
Versions of package r-cran-genabel |
Release | Version | Architectures |
bullseye | 1.8-0-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.8-0-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.8-0-3 | amd64,arm64,armhf,i386 |
stretch | 1.8-0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.8-0-1 | amd64,armel,armhf,i386 |
bookworm | 1.8-0-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.8-0-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
|
The package offers the R library GenABEL for the hunt of genetic contributions
to a disease (or any other pheonypical trait) by so called genome-wide
association analysis. Additional input commonly comes from DNA mircoarray
experiments, performed on every individual, that determine differences
(polymorphisms) in the population. GenABEL finds associations between
quantitative or binary traits and single-nucleiotide polymorphisms
(SNPs).
Package 'GenABEL’ was removed from the CRAN repository.
The code was obtained from the archive.
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r-cran-kaos
Encoding of Sequences Based on Frequency Matrix Chaos
|
Versions of package r-cran-kaos |
Release | Version | Architectures |
bookworm | 0.1.2-2 | all |
bullseye | 0.1.2-2 | all |
trixie | 0.1.2-2 | all |
sid | 0.1.2-2 | all |
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License: DFSG free
|
Sequences encoding by using the chaos game representation.
Löchel et al. (2019) .
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r-cran-phangorn
GNU R package for phylogenetic analysis
|
Versions of package r-cran-phangorn |
Release | Version | Architectures |
stretch | 2.1.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.4.0-2 | amd64,arm64,armhf,i386 |
bullseye | 2.5.5-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.11.1+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.11.1+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.11.1+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 2.12.1 |
|
License: DFSG free
|
phangorn is a tool for reconstructing phylogenies, using distance-based
methods, maximum parsimony or maximum likelihood, and performing Hadamard
conjugation. It also offers functions for comparing trees, phylogenetic models
or splits, simulating character data and performing congruence analysis.
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r-cran-phytools
GNU R phylogenetic tools for comparative biology
|
Versions of package r-cran-phytools |
Release | Version | Architectures |
sid | 2.3-0-1 | all |
buster | 0.6-60-1 | all |
bookworm | 1.5-1-1 | all |
trixie | 2.3-0-1 | all |
bullseye | 0.7-70-1 | all |
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License: DFSG free
|
A wide range of functions for phylogenetic analysis. Functionality is
concentrated in phylogenetic comparative biology, but also includes a
diverse array of methods for visualizing, manipulating, reading or
writing, and even inferring phylogenetic trees and data. Included among
the functions in phylogenetic comparative biology are various for
ancestral state reconstruction, model-fitting, simulation of phylogenies
and data, and multivariate analysis. There are a broad range of plotting
methods for phylogenies and comparative data which include, but are not
restricted to, methods for mapping trait evolution on trees, for
projecting trees into phenotypic space or a geographic map, and for
visualizing correlated speciation between trees. Finally, there are a
number of functions for reading, writing, analyzing, inferring,
simulating, and manipulating phylogenetic trees and comparative data not
covered by other packages. For instance, there are functions for
randomly or non-randomly attaching species or clades to a phylogeny, for
estimating supertrees or consensus phylogenies from a set, for
simulating trees and phylogenetic data under a range of models, and for
a wide variety of other manipulations and analyses that phylogenetic
biologists might find useful in their research.
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r-cran-pscbs
R package: Analysis of Parent-Specific DNA Copy Numbers
|
Versions of package r-cran-pscbs |
Release | Version | Architectures |
buster | 0.64.0-1 | all |
bullseye | 0.65.0-3 | all |
sid | 0.67.0-3 | all |
trixie | 0.67.0-3 | all |
bookworm | 0.66.0-2 | all |
stretch | 0.62.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
Segmentation of allele-specific DNA copy number data and detection of regions
with abnormal copy number within each parental chromosome. Both tumor-normal
paired and tumoronly analyses are supported.
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r-cran-qtl
GNU R package for genetic marker linkage analysis
|
Versions of package r-cran-qtl |
Release | Version | Architectures |
bullseye | 1.47-9-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.44-9-1 | amd64,arm64,armhf,i386 |
jessie | 1.33-7-1 | amd64,armel,armhf,i386 |
bookworm | 1.58-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.40-8-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 1.70-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.70-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package r-cran-qtl: |
devel | lang:r, library |
field | biology, statistics |
role | app-data |
suite | gnu |
|
License: DFSG free
|
R/qtl is an extensible, interactive environment for mapping quantitative
trait loci (QTLs) in experimental crosses. It is implemented as an
add-on-package for the freely available and widely used statistical
language/software R (see http://www.r-project.org).
The development of this software as an add-on to R allows one to take
advantage of the basic mathematical and statistical functions, and
powerful graphics capabilities, that are provided with R. Further,
the user will benefit by the seamless integration of the QTL mapping
software into a general statistical analysis program. The goal is to
make complex QTL mapping methods widely accessible and allow users to
focus on modeling rather than computing.
A key component of computational methods for QTL mapping is the hidden
Markov model (HMM) technology for dealing with missing genotype data. The
main HMM algorithms, with allowance for the presence of genotyping errors,
for backcrosses, intercrosses, and phase-known four-way crosses
were implemented.
The current version of R/qtl includes facilities for estimating
genetic maps, identifying genotyping errors, and performing single-QTL
genome scans and two-QTL, two-dimensional genome scans, by interval
mapping (with the EM algorithm), Haley-Knott regression, and multiple
imputation. All of this may be done in the presence of covariates (such
as sex, age or treatment). One may also fit higher-order QTL models by
multiple imputation.
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r-cran-rotl
GNU R interface to the 'Open Tree of Life' API
|
Versions of package r-cran-rotl |
Release | Version | Architectures |
bookworm | 3.0.14-1 | all |
trixie | 3.1.0-1 | all |
stretch | 3.0.1-1 | all |
bullseye | 3.0.11-1 | all |
buster | 3.0.6-1 | all |
sid | 3.1.0-1 | all |
|
License: DFSG free
|
An interface to the 'Open Tree of Life' API to retrieve phylogenetic
trees, information about studies used to assemble the synthetic tree,
and utilities to match taxonomic names to 'Open Tree identifiers'. The
'Open Tree of Life' aims at assembling a comprehensive phylogenetic tree
for all named species.
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r-cran-samr
GNU R significance analysis of microarrays
|
Versions of package r-cran-samr |
Release | Version | Architectures |
bookworm | 3.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 3.0-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 3.0-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 3.0-1 | amd64,arm64,armhf,i386 |
bullseye | 3.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
This GNU R package provides significance analysis of microarrays.
A microarray is a multiplex lab-on-a-chip. It is a 2D array on a solid
substrate (usually a glass slide or silicon thin-film cell) that assays
large amounts of biological material using high-throughput screening
miniaturized, multiplexed and parallel processing and detection methods.
This package helps analysing this kind of microarrays.
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r-cran-sdmtools
Species Distribution Modelling Tools
|
Versions of package r-cran-sdmtools |
Release | Version | Architectures |
sid | 1.1-221.2-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.1-221.2-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.1-221.2-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.1-221.2-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.1-221-1 | amd64,arm64,armhf,i386 |
|
License: DFSG free
|
This package provides a set of tools for post processing the
outcomes of species distribution modeling exercises. It includes novel
methods for comparing models and tracking changes in distributions through
time. It further includes methods for visualizing outcomes, selecting
thresholds, calculating measures of accuracy and landscape fragmentation
statistics, etc.
This package was made possible in part by financial
support from the Australian Research Council & ARC Research Network for
Earth System Science.
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r-cran-seqinr
GNU R biological sequences retrieval and analysis
|
Versions of package r-cran-seqinr |
Release | Version | Architectures |
buster | 3.4-5-2 | amd64,arm64,armhf,i386 |
trixie | 4.2-36-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 4.2-36-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 4.2-5-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 3.3-3-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 4.2-23-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
Exploratory data analysis and data visualization for biological sequence
(DNA and protein) data. Includes also utilities for sequence data
management under the ACNUC system.
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r-cran-seurat
Tools for Single Cell Genomics
|
Versions of package r-cran-seurat |
Release | Version | Architectures |
bookworm | 4.3.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 5.1.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 4.0.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
A toolkit for quality control, analysis, and exploration of single cell
RNA sequencing data. 'Seurat' aims to enable users to identify and
interpret sources of heterogeneity from single cell transcriptomic
measurements, and to integrate diverse types of single cell data. See
Satija R, Farrell J, Gennert D, et al (2015) ,
Macosko E, Basu A, Satija R, et al (2015)
, and Butler A and Satija R (2017)
for more details.
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r-cran-shazam
Immunoglobulin Somatic Hypermutation Analysis
|
Versions of package r-cran-shazam |
Release | Version | Architectures |
bullseye | 1.0.2-1 | all |
sid | 1.2.0-1 | all |
buster | 0.1.11-1 | all |
bookworm | 1.1.2-1 | all |
trixie | 1.2.0-1 | all |
|
License: DFSG free
|
Provides a computational framework for Bayesian estimation of
antigen-driven selection in immunoglobulin (Ig) sequences, providing an
intuitive means of analyzing selection by quantifying the degree of
selective pressure. Also provides tools to profile mutations in Ig
sequences, build models of somatic hypermutation (SHM) in Ig sequences,
and make model-dependent distance comparisons of Ig repertoires.
SHazaM is part of the Immcantation analysis framework for Adaptive
Immune Receptor Repertoire sequencing (AIRR-seq) and provides tools for
advanced analysis of somatic hypermutation (SHM) in immunoglobulin (Ig)
sequences. Shazam focuses on the following analysis topics:
- Quantification of mutational load
SHazaM includes methods for determine the rate of observed and
expected mutations under various criteria. Mutational profiling
criteria include rates under SHM targeting models, mutations specific
to CDR and FWR regions, and physicochemical property dependent
substitution rates.
- Statistical models of SHM targeting patterns
Models of SHM may be divided into two independent components:
1) a mutability model that defines where mutations occur and
2) a nucleotide substitution model that defines the resulting mutation.
Collectively these two components define an SHM targeting
model. SHazaM provides empirically derived SHM 5-mer context mutation
models for both humans and mice, as well tools to build SHM targeting
models from data.
- Analysis of selection pressure using BASELINe
The Bayesian Estimation of Antigen-driven Selection in Ig Sequences
(BASELINe) method is a novel method for quantifying antigen-driven
selection in high-throughput Ig sequence data. BASELINe uses SHM
targeting models can be used to estimate the null distribution of
expected mutation frequencies, and provide measures of selection
pressure informed by known AID targeting biases.
- Model-dependent distance calculations
SHazaM provides methods to compute evolutionary distances between
sequences or set of sequences based on SHM targeting models. This
information is particularly useful in understanding and defining
clonal relationships.
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r-cran-spp
GNU R ChIP-seq processing pipeline
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Versions of package r-cran-spp |
Release | Version | Architectures |
trixie | 1.16.0-2 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
buster | 1.15.5-1 | amd64,arm64,armhf,i386 |
bullseye | 1.16.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.16.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.16.0-2 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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R package for anlaysis of ChIP-seq and other functional sequencing data
- Assess overall DNA-binding signals in the data and select appropriate
quality of tag alignment.
- Discard or restrict positions with abnormally high number of tags.
- Calculate genome-wide profiles of smoothed tag density and save them
in WIG files for viewing in other browsers.
- Calculate genome-wide profiles providing conservative statistical
estimates of fold enrichment ratios along the genome. These can be
exported for browser viewing, or thresholded to determine regions of
significant enrichment/depletion.
- Determine statistically significant point binding positions
- Assess whether the set of point binding positions detected at a
current sequencing depth meets saturation criteria, and if does not,
estimate what sequencing depth would be required to do so.
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r-cran-tcr
Advanced Data Analysis of Immune Receptor Repertoires
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Versions of package r-cran-tcr |
Release | Version | Architectures |
bookworm | 2.3.2+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.2.3-1 | amd64,arm64,armhf,i386 |
sid | 2.3.2+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 2.3.2+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.3.2+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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Cells of the immune system are the grand exception to the rule
that all cells of an individuum have (mostly exact) copies of the
same DNA. B cells (which produce antibodies) and T cells (which
communicate with cells) however have a section of their DNA with
genes of the groups V, D and J that are reorganised within the
genomic DNA to provide the flexibility to deal with yet unknown
pathogens.
This package provides a platform for the advanced analysis of T
cell receptor repertoire data and its visualisations.
Caveat: This package is soon to be replaced by
http://github.com/immunomind/immunarch which is not yet available
as a Debian package.
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r-cran-tigger
Infers new Immunoglobulin alleles from Rep-Seq Data
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Versions of package r-cran-tigger |
Release | Version | Architectures |
buster | 0.3.1-1 | all |
bookworm | 1.0.1-1 | all |
sid | 1.1.0-1 | all |
trixie | 1.1.0-1 | all |
bullseye | 1.0.0-1 | all |
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License: DFSG free
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Summary: Infers the V genotype of an individual from immunoglobulin (Ig)
repertoire-sequencing (Rep-Seq) data, including detection of any novel
alleles. This information is then used to correct existing V allele calls
from among the sample sequences.
High-throughput sequencing of B cell immunoglobulin receptors is
providing unprecedented insight into adaptive immunity. A key step in
analyzing these data involves assignment of the germline V, D and J gene
segment alleles that comprise each immunoglobulin sequence by matching
them against a database of known V(D)J alleles. However, this process
will fail for sequences that utilize previously undetected alleles,
whose frequency in the population is unclear.
TIgGER is a computational method that significantly improves V(D)J
allele assignments by first determining the complete set of gene segments
carried by an individual (including novel alleles) from V(D)J-rearrange
sequences. TIgGER can then infer a subject’s genotype from these
sequences, and use this genotype to correct the initial V(D)J allele
assignments.
The application of TIgGER continues to identify a surprisingly high
frequency of novel alleles in humans, highlighting the critical need
for this approach. TIgGER, however, can and has been used with data
from other species.
Core Abilities:
- Detecting novel alleles
- Inferring a subject’s genotype
- Correcting preliminary allele calls
Required Input
- A table of sequences from a single individual, with columns containing
the following:
- V(D)J-rearranged nucleotide sequence (in IMGT-gapped format)
- Preliminary V allele calls
- Preliminary J allele calls
- Length of the junction region
- Germline Ig sequences in IMGT-gapped fasta format (e.g., as those
downloaded from IMGT/GENE-DB)
The former can be created through the use of IMGT/HighV-QUEST and
Change-O.
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r-cran-treespace
Statistical Exploration of Landscapes of Phylogenetic Trees
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Versions of package r-cran-treespace |
Release | Version | Architectures |
bullseye | 1.1.4.0+dfsg-1 | amd64,arm64,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.1.4.1+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.1.4.3+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.1.4.3+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.1.3+dfsg-1 | amd64,arm64,armhf,i386 |
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License: DFSG free
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Tools for the exploration of distributions of phylogenetic trees.
This package includes a shiny interface which can be started from R using
'treespaceServer()'.
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r-cran-tsne
t-distributed stochastic neighbor embedding for R (t-SNE)
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Versions of package r-cran-tsne |
Release | Version | Architectures |
trixie | 0.1-3.1-1 | all |
bullseye | 0.1-3-3 | all |
bookworm | 0.1-3.1-1 | all |
sid | 0.1-3.1-1 | all |
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License: DFSG free
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A "pure R" implementation of the t-SNE algorithm.
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r-cran-vegan
Community Ecology Package for R
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Versions of package r-cran-vegan |
Release | Version | Architectures |
stretch | 2.4-2-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.5-7+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.6-4+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.6-8+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.6-8+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 2.0-10-1 | amd64,armel,armhf,i386 |
buster | 2.5-4+dfsg-3 | amd64,arm64,armhf,i386 |
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License: DFSG free
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R package for community ecologists. It contains most multivariate analysis
needed in analysing ecological communities, and tools for diversity analysis.
Most diversity methods assume that data are counts of individuals.
These tools are sometimes used outside the field of ecology, for instance to
study populations of white blood cells or RNA molecules.
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r-cran-webgestaltr
find over-represented properties in gene lists
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Versions of package r-cran-webgestaltr |
Release | Version | Architectures |
sid | 0.4.6-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.4.4-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.4.5-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.4.6-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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The web version WebGestalt http://www.webgestalt.org supports 12
organisms, 354 gene identifiers and 321,251 function categories. Users
can upload the data and functional categories with their own gene
identifiers. In addition to the Over-Representation Analysis, WebGestalt
also supports Gene Set Enrichment Analysis and Network Topology
Analysis. The user-friendly output report allows interactive and
efficient exploration of enrichment results. The WebGestaltR package not
only supports all above functions but also can be integrated into other
pipeline or simultaneously analyze multiple gene lists.
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r-cran-wgcna
Weighted Correlation Network Analysis
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Versions of package r-cran-wgcna |
Release | Version | Architectures |
bullseye | 1.69-1 | amd64,arm64,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.72-1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.73-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
sid | 1.73-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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Functions necessary to perform Weighted Correlation Network Analysis
on high-dimensional data as originally described in Horvath and Zhang
(2005) and Langfelder and Horvath (2008)
. Includes functions for rudimentary data
cleaning, construction of correlation networks, module identification,
summarization, and relating of variables and modules to sample
traits. Also includes a number of utility functions for data manipulation
and visualization.
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r-other-ascat
Allele-Specific Copy Number Analysis of Tumours
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Versions of package r-other-ascat |
Release | Version | Architectures |
bookworm | 3.1.1-1 | all |
trixie | 3.1.2-1 | all |
sid | 3.1.2-1 | all |
bullseye | 2.5.2-3 | all |
upstream | 3.2.0 |
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License: DFSG free
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ASCAT (allele-specific copy number analysis of tumors) is a allele-
specific copy number analysis of the in vivo breast cancer genome. It
can be used to accurately dissect the allele-specific copy number of
solid tumors, simultaneously estimating and adjusting for both tumor
ploidy and nonaberrant cell admixture.
Please cite:
Peter Van Loo, Silje H Nordgard, Ole Christian Lingjærde, Hege G Russnes, Inga H Rye, Wei Sun, Victor J Weigman, Peter Marynen, Anders Zetterberg, Bjørn Naume, Charles M Perou, Anne-Lise Børresen-Dale and Vessela N Kristensen:
Allele-specific Copy Number Analysis of Tumors.
(PubMed)
PNAS
107(39):16910-5
(2010)
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r-other-mott-happy.hbrem
GNU R package for fine-mapping complex diseases
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Versions of package r-other-mott-happy.hbrem |
Release | Version | Architectures |
bookworm | 2.4-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 2.4-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.4-1 | amd64,armel,armhf,i386 |
sid | 2.4-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 2.4-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 2.4-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.4-3 | amd64,arm64,armhf,i386 |
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License: DFSG free
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Happy is an R interface into the HAPPY C package for fine-mapping
Quantitative Trait Loci (QTL) in Heterogenous Stocks (HS). An HS is
an advanced intercross between (usually eight) founder inbred strains
of mice. HS are suitable for fine-mapping QTL. It uses a multipoint
analysis which offers significant improvements in statistical power to
detect QTLs over that achieved by single-marker association.
The happy package is
an extension of the original C program happy; it uses the C code to
compute the probability of descent from each of the founders, at each
locus position, but the happy packager allows a much richer range of
models to be fit to the data.
Read /usr/share/doc/r-other-mott-happy/README.Debian for a more
detailed explanation.
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r-other-rajewsky-dropbead
Basic Exploration and Analysis of Drop-seq Data
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Versions of package r-other-rajewsky-dropbead |
Release | Version | Architectures |
bullseye | 0.3.1+git20180221.d746c6f+ds-3 | all |
trixie | 0.3.1+git20180221.d746c6f+ds-3 | all |
sid | 0.3.1+git20180221.d746c6f+ds-3 | all |
bookworm | 0.3.1+git20180221.d746c6f+ds-3 | all |
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License: DFSG free
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Dropbead offers a quick and straightforward way to explore and perform
basic analysis of single cell sequencing data coming from droplet
sequencing. It has been particularly tailored for Drop-seq.
Please cite:
J. Alles, N. Karaiskos, S. Praktiknjo, S. Grosswendt, P. Wahle, P.-L. Ruffault, S. Ayoub, L. Schreyer, A. Boltengagen, C. Birchmeier, R. Zinzen an, C. Kocks and N. Rajewsky:
Cell fixation and preservation for droplet-based single-cell transcriptomics.
(PubMed,eprint)
BMC Biology
15(44)
(2017)
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racon
consensus module for raw de novo DNA assembly of long uncorrected reads
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Versions of package racon |
Release | Version | Architectures |
buster | 1.3.2-1 | amd64 |
bookworm | 1.5.0-3 | amd64,arm64,mips64el,ppc64el,s390x |
stretch-backports | 1.3.1-1~bpo9+1 | amd64 |
bullseye | 1.4.20-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.5.0-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch-backports-sloppy | 1.4.10-1~bpo9+1 | amd64 |
trixie | 1.5.0-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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Racon is intended as a standalone consensus module to correct raw
contigs generated by rapid assembly methods which do not include a
consensus step. The goal of Racon is to generate genomic consensus which
is of similar or better quality compared to the output generated by
assembly methods which employ both error correction and consensus steps,
while providing a speedup of several times compared to those methods. It
supports data produced by both Pacific Biosciences and Oxford Nanopore
Technologies.
Racon can be used as a polishing tool after the assembly with either
Illumina data or data produced by third generation of sequencing. The
type of data inputed is automatically detected.
Racon takes as input only three files: contigs in FASTA/FASTQ format,
reads in FASTA/FASTQ format and overlaps/alignments between the reads
and the contigs in MHAP/PAF/SAM format. Output is a set of polished
contigs in FASTA format printed to stdout. All input files can be
compressed with gzip.
Racon can also be used as a read error-correction tool. In this
scenario, the MHAP/PAF/SAM file needs to contain pairwise overlaps
between reads including dual overlaps.
A wrapper script is also available to enable easier usage to the end-
user for large datasets. It has the same interface as racon but adds
two additional features from the outside. Sequences can be subsampled
to decrease the total execution time (accuracy might be lower) while
target sequences can be split into smaller chunks and run sequentially
to decrease memory consumption. Both features can be run at the same
time as well.
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radiant
explore hierarchical metagenomic data with zoomable pie charts
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Versions of package radiant |
Release | Version | Architectures |
trixie | 2.8.1+dfsg-2 | all |
stretch-backports | 2.7+dfsg-2~bpo9+1 | all |
bookworm | 2.8.1+dfsg-2 | all |
buster | 2.7+dfsg-2 | all |
bullseye | 2.7.1+dfsg-4 | all |
sid | 2.8.1+dfsg-2 | all |
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License: DFSG free
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Krona allows hierarchical data to be explored with zoomable pie charts.
Krona charts include support for several bioinformatics tools and raw
data formats. The charts can be viewed with a recent version of any
major web browser.
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ragout
Reference-Assisted Genome Ordering UTility
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Versions of package ragout |
Release | Version | Architectures |
bookworm | 2.3-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.3-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.3-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 2.3-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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Ragout (Reference-Assisted Genome Ordering UTility) is a tool for
chromosome-level scaffolding using multiple references. Given initial
assembly fragments (contigs/scaffolds) and one or multiple related
references (complete or draft), it produces a chromosome-scale assembly
(as a set of scaffolds).
The approach is based on the analysis of genome rearrangements (like
inversions or chromosomal translocations) between the input genomes and
reconstructing the most parsimonious structure of the target genome.
Ragout now supports both small and large genomes (of mammalian scale
and complexity). The assembly of highly polymorphic genomes is
currently limited.
Please cite:
Mikhail Kolmogorov, Joel Armstrong, Brian J. Raney, Ian Streeter, Matthew Dunn, Fengtang Yang, Duncan Odom, Paul Flicek, Thomas M. Keane, David Thybert, Benedict Paten and Son Pham:
Chromosome assembly of large and complex genomes using multiple references.
(PubMed,eprint)
Genome Research
28(11):1720-1732
(2018)
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rambo-k
Read Assignment Method Based On K-mers
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Versions of package rambo-k |
Release | Version | Architectures |
stretch | 1.21+dfsg-1 | all |
trixie | 1.21+dfsg-5 | all |
bookworm | 1.21+dfsg-4 | all |
bullseye | 1.21+dfsg-3 | all |
buster | 1.21+dfsg-2 | all |
sid | 1.21+dfsg-5 | all |
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License: DFSG free
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RAMBO-K is a tool for rapid and sensitive removal of background sequences
from Next Generation Sequencing data.
RAMBO-K is a reference-based tool for rapid and sensitive extraction of
one organisms reads from a mixed dataset. It is based on a Markov chain
implementation, which uses genomic characteristics of each reference to
assign reads to the associated set.
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rampler
module for sampling genomic sequences
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Versions of package rampler |
Release | Version | Architectures |
stretch-backports | 1.1.0-1~bpo9+1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2.1.1-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.1.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.0.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.1.1-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.1.0-1 | amd64,arm64,armhf,i386 |
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License: DFSG free
|
Standalone module for sampling genomic sequences. It supports two modes,
random subsampling of sequencer data to a desired depth (given the
reference length) and file splitting to desired size in bytes.
Rampler takes as first input argument a file in FASTA/FASTQ format which
can be compressed with gzip. The rest of input parameters depend on the
mode of operation. The output is stored into a file(s) which is in the
same format as the input file but uncompressed.
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rapmap
rapid sensitive and accurate DNA read mapping via quasi-mapping
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Versions of package rapmap |
Release | Version | Architectures |
bookworm | 0.15.0+dfsg-3 | amd64 |
sid | 0.15.0+dfsg-4 | amd64 |
stretch | 0.4.0+dfsg-2 | amd64 |
buster | 0.12.0+dfsg-3 | amd64,arm64 |
bullseye | 0.15.0+dfsg-1 | amd64 |
trixie | 0.15.0+dfsg-4 | amd64 |
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License: DFSG free
|
RapMap is a testing ground for ideas in quasi-mapping / (lightweight /
pseudo) transcriptome alignment. That means that, at this point, it is
somewhat experimental. The develop branch will have the latest
improvements and additions, but is not guaranteed to be stable between
commits. Breaking changes to the master branch will be accompanied by a
tag to the version before the breaking change. Currently, RapMap is a
stand-alone quasi-mapper that can be used with other tools. It is also
being used as part of Sailfish and Salmon. Eventually, the hope is to
create and stabilize an API so that it can be used as a library from
other tools.
Quasi-mapping / (lightweight / pseudo)-alignment is the term that is
used here for the type of information required for certain tasks (e.g.
transcript quantification) that is less "heavyweight" than what is
provided by traditional alignment. For example, one may only need to
know the transcripts / contigs to which a read aligns and, perhaps, the
position within those transcripts rather than the optimal alignment and
base-for-base CIGAR string that aligns the read and substring of the
transcript. For details on RapMap (quasi-mapping in particular), please
check out the associated paper. Note: RapMap implements both quasi-
mapping and pseudo-alignment (originally introduced in Bray et al.
2016), these two are not the same thing. They are distinct concepts, and
RapMap simply happens to implement algorithms for computing both.
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rasmol
visualization of biological macromolecules
|
Versions of package rasmol |
Release | Version | Architectures |
bullseye | 2.7.6.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.7.6.0-1 | amd64,arm64,armhf,i386 |
jessie | 2.7.5.2-2 | amd64,armel,armhf,i386 |
bookworm | 2.7.6.0-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 2.7.5.2-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,s390x |
trixie | 2.7.6.0-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.7.6.0-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package rasmol: |
field | chemistry |
interface | x11 |
role | program |
scope | utility |
uitoolkit | gtk |
use | learning, viewing |
x11 | application |
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License: DFSG free
|
RasMol is a molecular graphics program intended for the visualisation of
proteins, nucleic acids and small molecules. The program is aimed at
display, teaching and generation of publication quality images.
The program reads in a molecule coordinate file and interactively displays
the molecule on the screen in a variety of colour schemes and molecule
representations. Currently available representations include depth-cued
wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres, ball and stick,
solid and strand biomolecular ribbons, atom labels and dot surfaces.
Supported input file formats include Protein Data Bank (PDB), Tripos
Associates' Alchemy and Sybyl Mol2 formats, Molecular Design Limited's
(MDL) Mol file format, Minnesota Supercomputer Center's (MSC) XYZ (XMol)
format, CHARMm format, CIF format and mmCIF format files.
This package installs two versions of RasMol, rasmol-gtk has a modern
GTK-based user interface and rasmol-classic is the version with the old
Xlib GUI.
The package is enhanced by the following packages:
rasmol-doc
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|
raster3d
tools for generating images of proteins or other molecules
|
Versions of package raster3d |
Release | Version | Architectures |
stretch | 3.0-3-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.0-7-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 3.0-7-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 3.0-7-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 3.0-7-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 3.0-3-1 | amd64,armel,armhf,i386 |
buster | 3.0-3-5 | amd64,arm64,armhf,i386 |
Debtags of package raster3d: |
field | biology, biology:structural |
interface | commandline |
role | program |
scope | application |
use | converting, viewing |
works-with | 3dmodel, image, image:raster |
works-with-format | jpg, png |
|
License: DFSG free
|
Raster3D is a set of tools for generating high quality raster images of
proteins or other molecules. The core program renders spheres, triangles,
cylinders, and quadric surfaces with specular highlighting, Phong shading,
and shadowing. It uses an efficient software Z-buffer algorithm which is
independent of any graphics hardware. Ancillary programs process atomic
coordinates from PDB files into rendering descriptions for pictures composed
of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can also be
used to render pictures composed in other programs such as Molscript in
glorious 3D with highlights, shadowing, etc. Output is to pixel image files
with 24 bits of color information per pixel.
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rate4site
detector of conserved amino-acid sites
|
Versions of package rate4site |
Release | Version | Architectures |
jessie | 3.0.0-1 | amd64,armel,armhf,i386 |
stretch | 3.0.0-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 3.0.0-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 3.0.0-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 3.0.0-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 3.0.0-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 3.0.0-6 | amd64,arm64,armhf,i386 |
|
License: DFSG free
|
Rate4Site calculates the relative evolutionary rate at each site using a
probabilistic-based evolutionary model.
This allows taking into account the stochastic process underlying sequence
evolution within protein families
and the phylogenetic tree of the proteins in the family.
The conservation score at a site corresponds to the site's evolutionary rate.
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raxml
Randomized Axelerated Maximum Likelihood of phylogenetic trees
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Versions of package raxml |
Release | Version | Architectures |
stretch | 8.2.9+dfsg-1 | amd64,i386 |
jessie | 8.1.1-3 | amd64,i386 |
buster | 8.2.12+dfsg-1 | amd64,i386 |
bullseye | 8.2.12+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 8.2.12+dfsg-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 8.2.13+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 8.2.13+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package raxml: |
field | biology |
role | program |
|
License: DFSG free
|
RAxML is a program for sequential and parallel Maximum Likelihood-based
inference of large phylogenetic trees. It has originally been derived
from fastDNAml.
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ray
de novo genome assemblies of next-gen sequencing data
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Versions of package ray |
Release | Version | Architectures |
jessie | 2.3.1-1 | amd64,armel,armhf,i386 |
bookworm | 2.3.1-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.3.1-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 2.3.1-6 | amd64,arm64,armhf,i386 |
bullseye | 2.3.1-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 2.3.1-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
Ray is a parallel software that computes de novo genome assemblies with
next-generation sequencing data.
Ray is written in C++ and can run in parallel on numerous interconnected
computers using the message-passing interface (MPI) standard.
Included:
- Ray de novo assembly of single genomes
- Ray Méta de novo assembly of metagenomes
- Ray Communities microbe abundance + taxonomic profiling
- Ray Ontologies gene ontology profiling
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rdp-alignment
Ribosomal Database Project (RDP) alignment tools package
|
Versions of package rdp-alignment |
Release | Version | Architectures |
bookworm | 1.2.0-8 | all |
buster | 1.2.0-5 | all |
bullseye | 1.2.0-6 | all |
stretch | 1.2.0-2 | all |
sid | 1.2.0-8 | all |
trixie | 1.2.0-8 | all |
|
License: DFSG free
|
The Alignment tools package contains commands to do defined community
analysis, pairwise alignment and hidden markov model (HMMER3 models,
no training).
The package also contains the AlignmentTools Java library which is used by
other RDP tools.
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rdp-classifier
extensible sequence classifier for fungal lsu, bacterial and archaeal 16s
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Versions of package rdp-classifier |
Release | Version | Architectures |
bookworm | 2.10.2-6 | all |
sid | 2.10.2-7 | all |
stretch | 2.10.2-1 | all |
buster | 2.10.2-4 | all |
bullseye | 2.10.2-5 | all |
trixie | 2.10.2-7 | all |
|
License: DFSG free
|
The RDP Classifier is a naive Bayesian classifier which was developed
to provide rapid taxonomic placement based on rRNA sequence data. The
RDP Classifier can rapidly and accurately classify bacterial and
archaeal 16s rRNA sequences, and Fungal LSU sequences. It provides
taxonomic assignments from domain to genus, with confidence estimates
for each assignment. The RDP Classifier likely can be adapted to
additional phylogenetically coherent bacterial taxonomies.
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rdp-readseq
Ribosomal Database Project (RDP) sequence reading and writing
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Versions of package rdp-readseq |
Release | Version | Architectures |
bullseye | 2.0.2-7 | all |
bookworm | 2.0.2-9 | all |
trixie | 2.0.2-9 | all |
sid | 2.0.2-9 | all |
stretch | 2.0.2-2 | all |
buster | 2.0.2-6 | all |
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License: DFSG free
|
Rdp-readseq is a simple user interface to the sequence reading library
developed by the Ribosomal Database Project. It can handle genbank, embl,
fasta, fastq, sff and sto files. It can read from files or streams, and
can handle indexing files.
The package also contains the ReadSeq Java library which is used by other
RDP tools.
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readseq
Conversion between sequence formats
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Versions of package readseq |
Release | Version | Architectures |
trixie | 1-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1-11 | amd64,armel,armhf,i386 |
stretch | 1-11 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1-13 | amd64,arm64,armhf,i386 |
bullseye | 1-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package readseq: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | converting |
works-with-format | plaintext |
|
License: DFSG free
|
Reads and writes nucleic/protein sequences in various
formats. Data files may have multiple sequences.
Readseq is particularly useful as it automatically detects many
sequence formats, and converts between them.
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readucks
Nanopore read de-multiplexer (read demux -> readux -> readucks, innit)
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Versions of package readucks |
Release | Version | Architectures |
sid | 0.0.3-6 | all |
bullseye | 0.0.3-2 | all |
bookworm | 0.0.3-5 | all |
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License: DFSG free
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This package is inspired by the demultiplexing options in
porechop but without the adapter trimming options - it just demuxes.
It uses the parasail library with its Python bindings to do
pairwise alignment which provides a considerable speed up over
the seqan library used by porechop due to its low-level use
of vector processor instructions.
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reapr
universal tool for genome assembly evaluation
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Versions of package reapr |
Release | Version | Architectures |
stretch | 1.0.18+dfsg-3 | amd64,arm64,armel,i386,mips64el,mipsel,ppc64el |
sid | 1.0.18+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.0.18+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
trixie | 1.0.18+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.0.18+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
buster | 1.0.18+dfsg-4 | amd64,arm64,armhf |
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License: DFSG free
|
REAPR is a tool that evaluates the accuracy of a genome assembly using mapped
paired end reads, without the use of a reference genome for comparison. It can
be used in any stage of an assembly pipeline to automatically break incorrect
scaffolds and flag other errors in an assembly for manual inspection. It
reports mis-assemblies and other warnings, and produces a new broken assembly
based on the error calls.
The software requires as input an assembly in FASTA format and paired reads
mapped to the assembly in a BAM file. Mapping information such as the fragment
coverage and insert size distribution is analysed to locate mis-assemblies.
REAPR works best using mapped read pairs from a large insert library (at least
1000bp). Additionally, if a short insert Illumina library is also available,
REAPR can combine this with the large insert library in order to score each
base of the assembly.
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recan
genetic distance plotting for recombination events analysis
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Versions of package recan |
Release | Version | Architectures |
sid | 0.5+dfsg-1 | all |
trixie | 0.5+dfsg-1 | all |
bookworm | 0.1.5+dfsg-2 | all |
bullseye | 0.1.2-2 | all |
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License: DFSG free
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recan is a Python package which allows one to construct genetic distance
plots to explore and discover recombination events in viral genomes.
This method has been previously implemented in desktop software
tools: RAT, Simplot and RDP4.
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relion
toolkit for 3D reconstructions in cryo-electron microscopy
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Versions of package relion |
Release | Version | Architectures |
bookworm | 3.1.3-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 3.1.3-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 3.1.0-4 | amd64,i386 |
trixie | 3.1.3-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 5.0.0 |
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License: DFSG free
|
RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone
computer program for Maximum A Posteriori refinement of (multiple) 3D
reconstructions or 2D class averages in cryo-electron microscopy.
RELION provides a GUI, several command-line tools in parallel (MPI) and serial
versions, optionally with CUDA/GPU support.
relion provides the serial and parallel (MPI) command-line tools without
CUDA/GPU support.
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relion-gui
toolkit for 3D reconstructions in cryo-electron microscopy (gui apps)
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Versions of package relion-gui |
Release | Version | Architectures |
bullseye | 3.1.0-4 | amd64,i386 |
sid | 3.1.3-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 3.1.3-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 3.1.3-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 5.0.0 |
|
License: DFSG free
|
RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone
computer program for Maximum A Posteriori refinement of (multiple) 3D
reconstructions or 2D class averages in cryo-electron microscopy.
RELION provides a GUI, several command-line tools in parallel (MPI) and serial
versions, optionally with CUDA/GPU support.
relion-gui provides the graphical user interface without CUDA/GPU support.
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repeatmasker-recon
finds repeat families from biological sequences
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Versions of package repeatmasker-recon |
Release | Version | Architectures |
buster | 1.08-4 | amd64,arm64,armhf,i386 |
sid | 1.08-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.08-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.08-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.08-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.08-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
|
The RECON package implements a de novo algorithm for the identification
of repeat families from biological sequences.
The program implements an approach for the de novo identification and
classification of repeat sequence families that is based on extensions
to the usual approach of single linkage clustering of local pairwise
alignments between genomic sequences. The extensions use multiple
alignment information to define the boundaries of individual copies of
the repeats and to distinguish homologous but distinct repeat element
families. When tested on the human genome, this approach was able to
properly identify and group known transposable elements. The program,
should be useful for first-pass automatic classification of repeats in
newly sequenced genomes.
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reprof
protein secondary structure and accessibility predictor
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Versions of package reprof |
Release | Version | Architectures |
stretch | 1.0.1-4 | all |
jessie | 1.0.1-1 | all |
buster | 1.0.1-6 | all |
bullseye | 1.0.1-7 | all |
bookworm | 1.0.1-8 | all |
trixie | 1.0.1-8 | all |
sid | 1.0.1-9 | all |
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License: DFSG free
|
'reprof' is an improved implementation of 'prof', a popular protein secondary
structure and accessibility predictor. Prediction is either
done from protein sequence alone or from an alignment - the latter should be
used for optimal performance.
This package provides the 'reprof' command. It is only a command line
interface to the functionality provided by the modules in
librg-reprof-bundle-perl.
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resfinder
identify acquired antimicrobial resistance genes
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Versions of package resfinder |
Release | Version | Architectures |
bullseye | 3.2-3 | all |
sid | 4.4.2-2 | all |
trixie | 4.4.2-2 | all |
bookworm | 4.3.0-1 | all |
upstream | 4.6.0 |
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License: DFSG free
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ResFinder identifies acquired antimicrobial resistance genes in total or
partial sequenced isolates of bacteria.
ResFinder that uses BLAST for identification of acquired antimicrobial
resistance genes in whole-genome data. As input, the method can use both
pre-assembled, complete or partial genomes, and short sequence reads
from four different sequencing platforms. The method was evaluated on
1862 GenBank files containing 1411 different resistance genes, as well
as on 23 de-novo-sequenced isolates.
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rna-star
ultrafast universal RNA-seq aligner
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Versions of package rna-star |
Release | Version | Architectures |
trixie | 2.7.11b+dfsg-2 | amd64,arm64,mips64el,ppc64el,riscv64 |
bookworm | 2.7.10b+dfsg-2 | amd64,arm64,mips64el,ppc64el |
bullseye | 2.7.8a+dfsg-2 | amd64,arm64,mips64el,ppc64el |
sid | 2.7.11b+dfsg-2 | amd64,arm64,mips64el,ppc64el,riscv64 |
buster | 2.7.0a+dfsg-1 | amd64,arm64 |
stretch | 2.5.2b+dfsg-1 | amd64,arm64,mips64el,ppc64el |
stretch-backports | 2.7.0a+dfsg-1~bpo9+1 | amd64,arm64,mips64el,ppc64el |
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License: DFSG free
|
Spliced Transcripts Alignment to a Reference (STAR) software based on a
previously undescribed RNA-seq alignment algorithm that uses sequential
maximum mappable seed search in uncompressed suffix arrays followed by
seed clustering and stitching procedure. STAR outperforms other aligners
by a factor of >50 in mapping speed, aligning to the human genome 550
million 2 × 76 bp paired-end reads per hour on a modest 12-core server,
while at the same time improving alignment sensitivity and precision. In
addition to unbiased de novo detection of canonical junctions, STAR can
discover non-canonical splices and chimeric (fusion) transcripts, and is
also capable of mapping full-length RNA sequences. Using Roche 454
sequencing of reverse transcription polymerase chain reaction amplicons,
the authors experimentally validated 1960 novel intergenic splice
junctions with an 80-90% success rate, corroborating the high precision
of the STAR mapping strategy.
The package is enhanced by the following packages:
multiqc
Topics: Sequence analysis
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rnahybrid
Fast and effective prediction of microRNA/target duplexes
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Versions of package rnahybrid |
Release | Version | Architectures |
bullseye | 2.1.2-6 | amd64,arm64,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.1.2-5 | amd64,arm64,armhf,i386 |
stretch | 2.1.2-1 | amd64,arm64,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.1.1-2 | amd64,armel,armhf,i386 |
sid | 2.1.2-8 | amd64,arm64,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 2.1.2-8 | amd64,arm64,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.1.2-7 | amd64,arm64,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package rnahybrid: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing |
|
License: DFSG free
|
RNAhybrid is a tool for finding the minimum free energy hybridisation of a
long and a short RNA. The hybridisation is performed in a kind of domain mode,
ie. The short sequence is hybridised to the best fitting part of the long one.
The tool is primarily meant as a means for microRNA target prediction.
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roary
high speed stand alone pan genome pipeline
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Versions of package roary |
Release | Version | Architectures |
stretch | 3.8.0+dfsg-1 | all |
sid | 3.13.0+dfsg-2 | all |
trixie | 3.13.0+dfsg-2 | all |
bullseye | 3.13.0+dfsg-1 | all |
buster | 3.12.0+dfsg-2 | all |
stretch-backports | 3.12.0+dfsg-2~bpo9+1 | all |
bookworm | 3.13.0+dfsg-1 | all |
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License: DFSG free
|
Roary is a high speed stand alone pan genome pipeline, which takes annotated
assemblies in GFF3 format (as produced, for instance, by Prokka) and calculates
the pan genome. Using a standard desktop PC, it can analyse datasets with
thousands of samples, something which is computationally infeasible with
existing methods, without compromising the quality of the results. 128 samples
can be analysed in under 1 hour using 1 GB of RAM and a single processor.
To perform this analysis using existing methods would take weeks and hundreds
of GB of RAM. Roary is not intended for meta-genomics or for comparing
extremely diverse sets of genomes.
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rockhopper
system for analyzing bacterial RNA-seq data
|
Versions of package rockhopper |
Release | Version | Architectures |
trixie | 2.0.3+dfsg2-4 | all |
sid | 2.0.3+dfsg2-4 | all |
bookworm | 2.0.3+dfsg2-3 | all |
|
License: DFSG free
|
Rockhopper is a comprehensive and user-friendly system for
computational analysis of bacterial RNA-seq data. As input, Rockhopper
takes RNA sequencing reads output by high-throughput sequencing
technology (FASTQ, QSEQ, FASTA, SAM, or BAM files). Rockhopper supports
the following tasks:
- Reference based transcript assembly (when one or more reference
genomes are available)
- Aligning reads to genomes
- Assembling transcripts
- Identifying transcript boundaries and novel transcripts such as
small RNAs
- De novo transcript assembly (when reference genomes are unavailable)
- Normalizing data from different experiments
- Quantifying transcript abundance
- Testing for differential gene expression
- Characterizing operon structures
- Visualizing results in a genome browser
The package is enhanced by the following packages:
multiqc
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roguenarok
versatile and scalable algorithm for rogue taxon identification
|
Versions of package roguenarok |
Release | Version | Architectures |
bullseye | 1.0-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.0-3 | amd64,arm64,armhf,i386 |
trixie | 1.0.1-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.0.1-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.0.1-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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RogueNaRok is a versatile and scalable algorithm for rogue taxon
identification. It also includes implementations of the maximum agreement
subtree, leaf stability index and taxonomic instability index.
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rsem
RNA-Seq by Expectation-Maximization
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Versions of package rsem |
Release | Version | Architectures |
bullseye | 1.3.3+dfsg-1 | amd64,arm64,mips64el,ppc64el,s390x |
sid | 1.3.3+dfsg-3 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
trixie | 1.3.3+dfsg-3 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.3.3+dfsg-2 | amd64,arm64,mips64el,ppc64el,s390x |
stretch | 1.2.31+dfsg-1 | amd64,arm64,mips64el,ppc64el,s390x |
buster | 1.3.1+dfsg-1 | amd64,arm64 |
|
License: DFSG free
|
RSEM is a software package for estimating gene and isoform expression
levels from RNA-Seq data. The RSEM package provides an user-friendly
interface, supports threads for parallel computation of the EM
algorithm, single-end and paired-end read data, quality scores,
variable-length reads and RSPD estimation. In addition, it provides
posterior mean and 95% credibility interval estimates for expression
levels. For visualization, It can generate BAM and Wiggle files in both
transcript-coordinate and genomic-coordinate. Genomic-coordinate files
can be visualized by both UCSC Genome browser and Broad Institute’s
Integrative Genomics Viewer (IGV). Transcript-coordinate files can be
visualized by IGV. RSEM also has its own scripts to generate transcript
read depth plots in pdf format. The unique feature of RSEM is, the read
depth plots can be stacked, with read depth contributed to unique reads
shown in black and contributed to multi-reads shown in red. In addition,
models learned from data can also be visualized. Last but not least,
RSEM contains a simulator.
The package is enhanced by the following packages:
multiqc
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rtax
Classification of sequence reads of 16S ribosomal RNA gene
|
Versions of package rtax |
Release | Version | Architectures |
buster | 0.984-6 | all |
stretch | 0.984-5 | all |
jessie | 0.984-2 | all |
sid | 0.984-8 | all |
trixie | 0.984-8 | all |
bookworm | 0.984-8 | all |
bullseye | 0.984-7 | all |
|
License: DFSG free
|
Short-read technologies for microbial community profiling are increasingly
popular, yet previous techniques for assigning taxonomy to paired-end reads
perform poorly. RTAX provides rapid taxonomic assignments of paired-end
reads using a consensus algorithm.
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runcircos-gui
|
Versions of package runcircos-gui |
Release | Version | Architectures |
bullseye | 0.0+git20200528.82dda8c-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.0+git20200528.82dda8c-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 0.0+git20180828.97703b9-1 | amd64,arm64,armhf,i386 |
stretch-backports | 0.0+git20180828.97703b9-1~bpo9+1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 0.0+git20200528.82dda8c-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.0+git20200528.82dda8c-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
runCircos-gui is a simple yet comprehensive crossplatform software to
execute Circos from a graphical user interface. The software eliminates
the need to use command line for running Circos without compremising the
power of complete commandline parameters and options.
runCircos-gui optimize running parameters (both toggle options & options
with arguments) and install Perl packages without using command line.
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saint
Significance Analysis of INTeractome
|
Versions of package saint |
Release | Version | Architectures |
buster | 2.5.0+dfsg-3 | amd64,arm64,armhf,i386 |
stretch | 2.5.0+dfsg-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 2.5.0+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.5.0+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 2.4.0+dfsg-1 | amd64,armel,armhf,i386 |
bookworm | 2.5.0+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.5.0+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
SAINT implements the scoring algorithm for protein-protein interaction
data using label free quantitative proteomics data in AP-MS experiments.
It was used for spectral count data in the yeast kinase interactome work
not incorporating control purification, as well as a generalized
implementation for spectral count data with and without control
purification.
Alternatively, you can also run SAINT in combination with ProHits.
The package was written for either doing analysis without or with
control IPs and
Please cite:
A. Breitkreutz, H. Choi, J.R. Sharom, L. Boucher, V. Neduva, B. Larsen, Z.Y. Lin, B.J. Breitkreutz, C. Stark, G. Liu, J. Ahn, D. Dewar-Darch, T. Reguly, X. Tang, R. Almeida, Z.S. Qin, T. Pawson, A.-C. Gingras, A.I. Nesvizhskii and M. Tyers:
A global protein kinase and phosphatase interaction network in yeast.
(PubMed)
Science
328(5981):1043-6
(2010)
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|
salmid
rapid Kmer based Salmonella identifier from sequence data
|
Versions of package salmid |
Release | Version | Architectures |
bullseye | 0.1.23-2 | all |
stretch-backports | 0.1.23-1~bpo9+1 | all |
sid | 0.1.23-5 | all |
buster | 0.1.23-1 | all |
bookworm | 0.1.23-5 | all |
trixie | 0.1.23-5 | all |
|
License: DFSG free
|
SalmID enables rapid confirmation of Salmonella spp. and subspp. from
sequence data. This is done by checking taxonomic ID of single isolate
samples. Currently only IDs Salmonella species and subspecies, and
some common contaminants (Listeria, Escherichia).
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salmon
wicked-fast transcript quantification from RNA-seq data
|
Versions of package salmon |
Release | Version | Architectures |
bookworm | 1.10.1+ds1-1 | amd64,arm64 |
stretch | 0.7.2+ds1-2 | amd64 |
buster | 0.12.0+ds1-1 | amd64 |
bullseye | 1.4.0+ds1-1 | amd64,arm64 |
sid | 1.10.2+ds1-1 | amd64,arm64 |
trixie | 1.10.2+ds1-1 | amd64,arm64 |
upstream | 1.10.3 |
|
License: DFSG free
|
Salmon is a wicked-fast program to produce a highly-accurate, transcript-level
quantification estimates from RNA-seq data. Salmon achieves is accuracy and
speed via a number of different innovations, including the use of lightweight
alignments (accurate but fast-to-compute proxies for traditional read
alignments) and massively-parallel stochastic collapsed variational inference.
The result is a versatile tool that fits nicely into many different pipelines.
For example, you can choose to make use of the lightweight alignments by
providing Salmon with raw sequencing reads, or, if it is more convenient, you
can provide Salmon with regular alignments (e.g. computed with your favorite
aligner), and it will use the same wicked-fast, state-of-the-art inference
algorithm to estimate transcript-level abundances for your experiment.
The package is enhanced by the following packages:
multiqc
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sambamba
tools for working with SAM/BAM data
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Versions of package sambamba |
Release | Version | Architectures |
bookworm | 1.0+dfsg-1 | amd64,arm64 |
sid | 1.0.1+dfsg-2 | amd64,arm64,riscv64 |
bullseye | 0.8.0-1 | amd64,arm64 |
|
License: DFSG free
|
Sambamba positions itself as a performant alternative
to samtools and provides tools for
- Powerful filtering with sambamba view --filter
- Picard-like SAM header merging in the merge tool
- Optional for operations on whole BAMs
- Fast copying of a region to a new file with the slice tool
- Duplicate marking/removal, using the Picard criteria
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samblaster
marks duplicates, extracts discordant/split reads
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Versions of package samblaster |
Release | Version | Architectures |
trixie | 0.1.26-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.1.26-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.1.26-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 0.1.24-2 | amd64,arm64,armhf,i386 |
bullseye | 0.1.26-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
Current "next-generation" sequencing technologies cannot tell what
exact sequence they will be reading. They take what is available. And
if some sequences are read very often, then this needs some extra
biomedical thinking. The genome could for instance be duplicated.
samblaster is a fast and flexible program for marking duplicates in
read-id grouped paired-end SAM files. It can also optionally output
discordant read pairs and/or split read mappings to separate SAM files,
and/or unmapped/clipped reads to a separate FASTQ file. When marking
duplicates, samblaster will require approximately 20MB of memory per
1M read pairs.
The package is enhanced by the following packages:
multiqc
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samclip
filter SAM file for soft and hard clipped alignments
|
Versions of package samclip |
Release | Version | Architectures |
bookworm | 0.4.0-4 | all |
trixie | 0.4.0-4 | all |
sid | 0.4.0-4 | all |
bullseye | 0.4.0-2 | all |
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License: DFSG free
|
Most short read aligners perform local alignment of reads to the
reference genome. Examples includes bwa mem, minimap2, and bowtie2
(unless in --end-to-end mode). This means the ends of the read may not
be part of the best alignment.
This can be caused by:
- adapter sequences (aren't in the reference)
- poor quality bases (mismatches only make the alignment score worse)
- structural variation in your sample compared to the reference
- reads overlapping the start and end of contigs (including
circular genomes)
Read aligners output a SAM file. Column 6 in this format stores the
CIGAR string. which describes which parts of the read aligned and which
didn't. The unaligned ends of the read can be "soft" or "hard" clipped,
denoted with S and H at each end of the CIGAR string. It is possible for
both types to be present, but that is not common. Soft and hard don't
mean anything biologically, they just refer to whether the full read
sequence is in the SAM file or not.
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samtools
processing sequence alignments in SAM, BAM and CRAM formats
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Versions of package samtools |
Release | Version | Architectures |
bullseye | 1.11-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 0.1.19-1 | amd64,armhf,i386 |
stretch | 1.3.1-3 | amd64,arm64,armel,i386,mips64el,mipsel,ppc64el |
stretch-backports | 1.7-2~bpo9+1 | amd64,arm64,armel,armhf,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.9-4 | amd64,arm64,armhf |
experimental | 1.21-0+exp1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.20-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.20-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.16.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 1.21 |
Debtags of package samtools: |
field | biology |
interface | commandline |
network | client |
role | program |
scope | utility |
uitoolkit | ncurses |
use | analysing, calculating, filtering |
works-with | biological-sequence |
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License: DFSG free
|
Samtools is a set of utilities that manipulate nucleotide sequence alignments
in the binary BAM format. It imports from and exports to the ascii SAM
(Sequence Alignment/Map) and CRAM formats, does sorting, merging and indexing,
and allows one to retrieve reads in any regions swiftly. It is designed to work
on a stream, and is able to open a BAM or CRAM (not SAM) file on a remote FTP
or HTTP server.
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savvy-util
conversion tool for SAV file format
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Versions of package savvy-util |
Release | Version | Architectures |
trixie | 2.1.0-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.1.0-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.1.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
Savvy is the official C++ interface for the SAV file format and offers
seamless support for BCF and VCF files.
The binary sav can be used to handle SAV filed.
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scoary
pangenome-wide association studies
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Versions of package scoary |
Release | Version | Architectures |
sid | 1.6.16-10 | all |
bullseye | 1.6.16-2 | all |
buster | 1.6.16-1 | all |
bookworm | 1.6.16-5 | all |
stretch-backports | 1.6.16-1~bpo9+1 | all |
trixie | 1.6.16-10 | all |
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License: DFSG free
|
Scoary is designed to take the gene_presence_absence.csv file from
Roary as well as a traits file created by the user and calculate the
associations between all genes in the accessory genome and the traits. It
reports a list of genes sorted by strength of association per trait.
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scrappie
basecaller for Nanopore sequencer
|
Versions of package scrappie |
Release | Version | Architectures |
trixie | 1.4.2-8 | amd64,arm64,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.4.2-8 | amd64,arm64,armhf,i386,mips64el,ppc64el,s390x |
sid | 1.4.2-8 | amd64,arm64,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.4.2-7 | amd64,arm64,armhf,i386,mips64el,ppc64el,s390x |
experimental | 1.4.2-9~0exp0simde | amd64,arm64,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
|
The Nanopore is a device for DNA/RNA sequencing that does
not require an amplification of the material. The polynucleotides
are threaded through a pore and while these pass through,
the change in the electrostatic potential allows one to
identify ("call") the actual base that resides in the pore.
Scrappie goes a step further and also attempts to describe
modifications to the nucleic acid.
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scrm
simulator of evolution of genetic sequences
|
Versions of package scrm |
Release | Version | Architectures |
bullseye | 1.7.4-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.7.2-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.7.3-1 | amd64,arm64,armhf,i386 |
sid | 1.7.4-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.7.4-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.7.4-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
|
scrm simulates the evolution of genetic sequences.
It takes a neutral evolutionary model as input, and generates random sequences
that evolved under the model. As coalescent simulator, it traces the ancestry
of the sampled sequences backwards in time and is therefore extremely
efficient. Compared to other coalescent simulators, it can simulate
chromosome-scale sequences without a measureable reduction of genetic linkage
between different sites.
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scythe
Bayesian adaptor trimmer for sequencing reads
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Versions of package scythe |
Release | Version | Architectures |
sid | 0.994+git20141017.20d3cff-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.994+git20141017.20d3cff-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.994+git20141017.20d3cff-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.994+git20141017.20d3cff-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.994+git20141017.20d3cff-1 | amd64,arm64,armhf,i386 |
stretch | 0.994-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
Scythe uses a Naive Bayesian approach to classify contaminant substrings in
sequence reads. It considers quality information, which can make it robust in
picking out 3'-end adapters, which often include poor quality bases.
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seaview
Multiplatform interface for sequence alignment and phylogeny
|
Versions of package seaview |
Release | Version | Architectures |
bullseye | 5.0.4-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 5.0.5-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 5.0.5-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 5.0.5-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 4.7-1 | amd64,arm64,armhf,i386 |
stretch | 4.6.1.2-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 4.5.3.1-2 | amd64,armel,armhf,i386 |
Debtags of package seaview: |
field | biology, biology:bioinformatics |
interface | x11 |
network | client |
role | program |
scope | utility |
uitoolkit | fltk |
use | comparing, editing, printing, viewing |
works-with | biological-sequence |
works-with-format | plaintext |
x11 | application |
|
License: DFSG free
|
SeaView is a viewer and editor of multiple sequence alignments, i.e.
DNA or protein sequences are positioned each in their own separate line,
such that the nucleotide/amino acid at a particular position (column) is
presumed to have the same biochemical property.
SeaView reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA,
PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic trees.
Alignments can be manually edited. It drives the programs Muscle or Clustal
Omega for multiple sequence alignment, and also allows one to use any external
alignment algorithm able to read and write FASTA-formatted files. It computes
phylogenetic trees by parsimony using PHYLIP's dnapars/protpars algorithm, by
distance with NJ or BioNJ algorithms on a variety of evolutionary distances, or
by maximum likelihood using the program PhyML 3.0.
SeaView draws phylogenetic
trees on screen or PostScript files, and allows one to download sequences from
EMBL/GenBank/UniProt using the Internet.
The package is enhanced by the following packages:
muscle
muscle3
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seer
genomic sequence element (kmer) enrichment analysis
|
Versions of package seer |
Release | Version | Architectures |
bookworm | 1.1.4-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.1.4-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.1.4-2 | amd64,arm64,armhf,i386 |
stretch-backports | 1.1.4-2~bpo9+1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 1.1.2-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.1.4-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.1.4-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
Bacterial genomes vary extensively in terms of both gene content and
gene sequence - this plasticity hampers the use of traditional SNP-based
methods for identifying all genetic associations with phenotypic
variation. SEER provides a computationally scalable and widely
applicable statistical method for the identification of sequence
elements that are significantly enriched in a phenotype of interest.
SEER is applicable to even tens of thousands of genomes by counting variable-
length k-mers using a distributed string-mining algorithm. Robust
options are provided for association analysis that also correct for the
clonal population structure of bacteria. Using large collections of
genomes of the major human pathogen Streptococcus pneumoniae, SEER
identifies relevant previously characterised resistance determinants for
several antibiotics.
Please cite:
John A Lees, Minna Vehkala, Niko Välimäki, Simon R Harris, Claire Chewapreecha, Nicholas J Croucher, Pekka Marttinen, Mark R Davies, Andrew C Steer, Stephen Y C Tong, Antti Honkela, Julian Parkhill, Stephen D Bentley and Jukka Corander:
Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes.
(eprint)
bioRxiv
(2016)
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segemehl
short read mapping with gaps
|
Versions of package segemehl |
Release | Version | Architectures |
sid | 0.3.4-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.3.4-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.3.4-1 | amd64,arm64,armhf |
bookworm | 0.3.4-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.3.4-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
Segemehl is a software to map short sequencer reads to reference
genomes. Segemehl implements a matching strategy based on enhanced
suffix arrays (ESA). Segemehl accepts fasta and fastq queries (gzip'ed
and bgzip'ed). In addition to the alignment of reads from standard DNA-
and RNA-seq protocols, it also allows the mapping of bisulfite converted
reads (Lister and Cokus) and implements a split read mapping strategy.
The output of segemehl is a SAM or BAM formatted alignment file. In the
case of split-read mapping, additional BED files are written to the
disc. These BED files may be summarized with the postprocessing tool
haarz. In the case of the alignment of bisulfite converted reads, raw
methylation rates may also be called with haarz.
In brief, for each suffix of a read, segemehl aims to find the
best-scoring seed. Seeds might contain insertions, deletions, and
mismatches (differences). The number of differences allowed within a
single seed is user-controlled and is crucial for the runtime of the
program. Subsequently, seeds that undercut the user-defined E-value are
passed on to an exact semi-global alignment procedure. Finally, reads
with a minimum accuracy of percent are reported to the user.
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sepp
phylogeny with ensembles of Hidden Markov Models
|
Versions of package sepp |
Release | Version | Architectures |
sid | 4.5.5+dfsg-1 | amd64,arm64 |
bullseye | 4.3.10+dfsg-5 | amd64 |
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License: DFSG free
|
The tool SEPP implementing these methods uses ensembles of Hidden Markov
Models (HMMs) in different ways, each focusing on a different problem.
SEPP stands for "SATe-enabled Phylogenetic Placement", and addresses the
problem of phylogenetic placement of short reads into reference
alignments and trees.
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seqan-apps
C++ library for the analysis of biological sequences
|
Versions of package seqan-apps |
Release | Version | Architectures |
stretch | 2.3.1+dfsg-4 | amd64,arm64,i386,mips64el,ppc64el,s390x |
experimental | 2.5.0~rc3+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.4.1+dfsg-2 | amd64,armhf,i386 |
sid | 2.4.0+dfsg-16 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 2.4.0+dfsg-16 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 2.4.0+dfsg-11 | amd64,arm64,armhf,i386 |
stretch-backports | 2.4.0+dfsg-11~bpo9+1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.4.0+dfsg-15 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.4.0+dfsg-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package seqan-apps: |
devel | library |
|
License: DFSG free
|
SeqAn is a C++ template library of efficient algorithms and data
structures for the analysis of sequences with the focus on
biological data. This library applies a unique generic design that
guarantees high performance, generality, extensibility, and
integration with other libraries. SeqAn is easy to use and
simplifies the development of new software tools with a minimal loss
of performance. This package contains the applications dfi, pair_align,
micro_razers, seqan_tcoffee, seqcons, razers and tree_recon.
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seqan-needle
pre-filter for the counting of very large collections of nucleotide sequences
|
Versions of package seqan-needle |
Release | Version | Architectures |
sid | 1.0.3+ds-1 | amd64,arm64,mips64el,ppc64el,riscv64 |
trixie | 1.0.3+ds-1 | amd64,arm64,mips64el,ppc64el,riscv64 |
bookworm | 1.0.1.0.0.git.3011926+ds-4 | amd64,arm64,mips64el,ppc64el |
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License: DFSG free
|
Needle is a tool for semi-quantitative analysis of very large collections of
nucleotide sequences.
Needle stores its data in multiple interleaved Bloom filter, a fast and space
efficient probabilistic data structure and uses a windowing scheme (also called
minimisers) to reduce the amount of data to store. How many interleaved Bloom
filter are used is defined by the user. Each interleaved Bloom filter has a so
called expression threshold and stores minimisers with an occurrence greater
than or equal to its own expression threshold and smaller than the next biggest
expression threshold (if there is no bigger expression threshold, all greater
than or equal to the threshold are stored). These expression thresholds are
then used during the query (called estimate) to approximate the expression
values of given transcripts.
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seqan-raptor
pre-filter for querying very large collections of nucleotide sequences
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Versions of package seqan-raptor |
Release | Version | Architectures |
trixie | 3.0.1+ds-5 | amd64,arm64,mips64el,ppc64el,riscv64 |
sid | 3.0.1+ds-5 | amd64,arm64,mips64el,ppc64el,riscv64 |
bookworm | 2.0.0.0.git.fecfbca+ds-3 | amd64,arm64,mips64el,ppc64el |
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License: DFSG free
|
Raptor is a system for approximately searching many queries such as
next-generation sequencing reads or transcripts in large collections of
nucleotide sequences. Raptor uses winnowing minimizers to define a set of
representative k-mers, an extension of the interleaved Bloom filters (IBFs) as
a set membership data structure and probabilistic thresholding for minimizers.
This approach allows compression and partitioning of the IBF to enable the
effective use of secondary memory.
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seqkit
cross-platform and ultrafast toolkit for FASTA/Q file manipulation
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Versions of package seqkit |
Release | Version | Architectures |
sid | 2.8.2+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.3.1+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.15.0+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.8.2+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 2.9.0 |
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License: DFSG free
|
SeqKit describes a cross-platform ultrafast comprehensive toolkit for
FASTA/Q processing. SeqKit provides executable binary files for all
major operating systems, including Windows, Linux, and Mac OS X, and can
be directly used without any dependencies or pre-configurations. SeqKit
demonstrates competitive performance in execution time and memory usage
compared to similar tools. The efficiency and usability of SeqKit enable
researchers to rapidly accomplish common FASTA/Q file manipulations.
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seqmagick
imagemagick-like frontend to Biopython SeqIO
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Versions of package seqmagick |
Release | Version | Architectures |
sid | 0.8.6-3 | all |
buster | 0.7.0-1 | all |
bullseye | 0.8.4-1 | all |
bookworm | 0.8.4-3 | all |
trixie | 0.8.6-3 | all |
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License: DFSG free
|
Seqmagick is a little utility to expose the file format conversion
in BioPython in a convenient way.
Features include:
- Modifying sequences:
- Remove gaps
- Reverse & reverse complement
- Trim to a range of residues
- Change case
- Sort by length or ID
- Displaying information about sequence files
- Subsetting sequence files by:
- Position
- ID
- Deduplication
- Filtering sequences by quality score
- Trimming alignments to a region of interest defined by the forward
and reverse primers
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seqprep
stripping adaptors and/or merging paired reads of DNA sequences with overlap
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Versions of package seqprep |
Release | Version | Architectures |
trixie | 1.3.2-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.3.2-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.3.2-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.3.2-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.3.2-3 | amd64,arm64,armhf,i386 |
sid | 1.3.2-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
|
SeqPrep is a program to merge paired end Illumina reads that are overlapping
into a single longer read. It may also just be used for its adapter trimming
feature without doing any paired end overlap. When an adapter sequence is
present, that means that the two reads must overlap (in most cases) so they
are forcefully merged. When reads do not have adapter sequence they must be
treated with care when doing the merging, so a much more specific approach is
taken. The default parameters were chosen with specificity in mind, so that
they could be ran on libraries where very few reads are expected to overlap.
It is always safest though to save the overlapping procedure for libraries
where you have some prior knowledge that a significant portion of the reads
will have some overlap.
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seqsero
Salmonella serotyping from genome sequencing data
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Versions of package seqsero |
Release | Version | Architectures |
sid | 1.0.1+dfsg-6 | amd64,arm64 |
stretch-backports | 1.0-2~bpo9+1 | all |
buster | 1.0.1+dfsg-1 | all |
bullseye | 1.0.1+dfsg-4 | all |
bookworm | 1.0.1+dfsg-6 | amd64,arm64 |
trixie | 1.0.1+dfsg-6 | amd64,arm64 |
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License: DFSG free
|
SeqSero is a pipeline for Salmonella serotype determination from raw
sequencing reads or genome assemblies.
SeqSero is a novel tool for determining Salmonella serotypes using high-
throughput genome sequencing data. SeqSero is based on curated databases
of Salmonella serotype determinants (rfb gene cluster, fliC and fljB
alleles) and is predicted to determine serotype rapidly and accurately
for nearly the full spectrum of Salmonella serotypes (more than 2,300
serotypes), from both raw sequencing reads and genome assemblies. The
performance of SeqSero was evaluated by testing
1. raw reads from genomes of 308 Salmonella isolates of known serotype
2. raw reads from genomes of 3,306 Salmonella isolates sequenced and
made publicly available by GenomeTrakr, a U.S. national monitoring
network operated by the Food and Drug Administration; and
3. 354 other publicly available draft or complete Salmonella genomes.
SeqSero can help to maintain the well-established utility of Salmonella
serotyping when integrated into a platform of WGS-based pathogen
subtyping and characterization.
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seqtk
Fast and lightweight tool for processing sequences in the FASTA or FASTQ format
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Versions of package seqtk |
Release | Version | Architectures |
bookworm | 1.3-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.0-1 | amd64,armel,armhf,i386 |
bullseye | 1.3-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.3-1 | amd64,arm64,armhf,i386 |
trixie | 1.4-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.4-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.2-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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Currently, seqtk supports quality based trimming with the phred
algorithm, converting fastq to fasta, reverse complementing sequences,
extracting or masking subsequences in regions given in a BED/name list
file, and more. It contains a subsampling module to sample exactly n
sequences or a fraction of sequences.
Seqtk supports both fasta and fastq input files, which can be
optionally gzip compressed.
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sga
de novo genome assembler that uses string graphs
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Versions of package sga |
Release | Version | Architectures |
trixie | 0.10.15-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
sid | 0.10.15-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
bookworm | 0.10.15-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
bullseye | 0.10.15-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
buster | 0.10.15-4 | amd64,arm64 |
stretch | 0.10.15-2 | amd64,arm64,mips64el,ppc64el |
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License: DFSG free
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The major goal of SGA is to be very memory efficient, which is achieved by
using a compressed representation of DNA sequence reads.
SGA is a de novo assembler for DNA sequence reads. It is based on Gene Myers'
string graph formulation of assembly and uses the FM-index/Burrows-Wheeler
transform to efficiently find overlaps between sequence reads.
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shasta
nanopore whole genome assembly (binaries and scripts)
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Versions of package shasta |
Release | Version | Architectures |
trixie | 0.12.0-1 | amd64,arm64 |
experimental | 0.12.0-2 | amd64,arm64 |
bookworm | 0.11.1-1 | amd64,arm64 |
bullseye | 0.7.0-3 | amd64,arm64 |
sid | 0.12.0-1 | amd64,arm64 |
upstream | 0.13.0 |
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License: DFSG free
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De novo assembly from Oxford Nanopore reads. The goal of the Shasta long
read assembler is to rapidly produce accurate assembled sequence using
as input DNA reads generated by Oxford Nanopore flow cells.
Computational methods used by the Shasta assembler include:
-
Using a run-length representation of the read sequence. This makes
the assembly process more resilient to errors in homopolymer
repeat counts, which are the most common type of errors in Oxford
Nanopore reads.
-
Using in some phases of the computation a representation of the read
sequence based on markers, a fixed subset of short k-mers (k ≈ 10).
Shasta assembly quality is comparable or better than assembly quality
achieved by other long read assemblers.
This package contains the executable binaries (tools) and
accommodating scripts.
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shovill
Assemble bacterial isolate genomes from Illumina paired-end reads
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Versions of package shovill |
Release | Version | Architectures |
bookworm | 1.1.0-9 | amd64 |
trixie | 1.1.0-9 | amd64 |
bullseye | 1.1.0-4 | amd64 |
sid | 1.1.0-9 | amd64 |
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License: DFSG free
|
Shovill is a pipeline which uses SPAdes at its core,
but alters the steps before and after the primary
assembly step to get similar results in less time.
Shovill also supports other assemblers like SKESA,
Velvet and Megahit, so you can take advantage of the
pre- and post-processing the Shovill provides
with those too.
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sibelia
comparative genomics tool
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Versions of package sibelia |
Release | Version | Architectures |
experimental | 3.0.7+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 3.0.7+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 3.0.7+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 3.0.7+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 3.0.7+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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Sibelia (Synteny Block ExpLoration tool) is a comparative genomics tool:
It assists biologists in analysing the genomic variations that correlate
with pathogens, or the genomic changes that help microorganisms adapt in
different environments. Sibelia will also be helpful for the
evolutionary and genome rearrangement studies for multiple strains of
microorganisms.
Sibelia is useful in finding:
1) shared regions,
2) regions that present in one group of genomes but not in others,
3) rearrangements that transform one genome to other genomes.
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sibsim4
align expressed RNA sequences on a DNA template
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Versions of package sibsim4 |
Release | Version | Architectures |
bookworm | 0.20-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.20-4 | amd64,arm64,armhf,i386 |
stretch | 0.20-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 0.20-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.20-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 0.20-2 | amd64,armel,armhf,i386 |
bullseye | 0.20-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package sibsim4: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | comparing, searching |
works-with-format | plaintext |
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License: DFSG free
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The SIBsim4 project is based on sim4, which is a program designed to align
an expressed DNA sequence with a genomic sequence, allowing for introns.
SIBsim4 is a fairly extensive rewrite of the original code with the following
goals:
- speed improvement;
- allow large, chromosome scale, DNA sequences to be used;
- provide more detailed output about splice types;
- provide more detailed output about polyA sites;
- misc code cleanups and fixes.
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sickle
windowed adaptive trimming tool for FASTQ files using quality
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Versions of package sickle |
Release | Version | Architectures |
trixie | 1.33+git20150314.f3d6ae3-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.33-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.33+git20150314.f3d6ae3-1 | amd64,arm64,armhf,i386 |
bullseye | 1.33+git20150314.f3d6ae3-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.33+git20150314.f3d6ae3-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.33+git20150314.f3d6ae3-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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Most modern sequencing technologies produce reads that have deteriorating
quality towards the 3'-end. Incorrectly called bases here negatively impact
assembles, mapping, and downstream bioinformatics analyses.
Sickle is a tool that uses sliding windows along with quality and length
thresholds to determine when quality is sufficiently low to trim the 3'-end
of reads. It will also discard reads based upon the length threshold. It takes
the quality values and slides a window across them whose length is 0.1 times
the length of the read. If this length is less than 1, then the window is set
to be equal to the length of the read. Otherwise, the window slides along the
quality values until the average quality in the window drops below the
threshold. At that point the algorithm determines where in the window the drop
occurs and cuts both the read and quality strings there. However, if the cut
point is less than the minimum length threshold, then the read is discarded
entirely.
Sickle supports four types of quality values: Illumina, Solexa, Phred, and
Sanger. Note that the Solexa quality setting is an approximation (the actual
conversion is a non-linear transformation). The end approximation is close.
Sickle also supports gzipped file inputs.
The package is enhanced by the following packages:
multiqc
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sigma-align
Simple greedy multiple alignment of non-coding DNA sequences
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Versions of package sigma-align |
Release | Version | Architectures |
stretch | 1.1.3-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.1.3-6 | amd64,arm64,armhf,i386 |
bullseye | 1.1.3-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.1.3-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.1.3-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.1.3-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.1.3-3 | amd64,armel,armhf,i386 |
Debtags of package sigma-align: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing, comparing |
works-with-format | plaintext |
|
License: DFSG free
|
Sigma (“Simple greedy multiple alignment”) is an alignment program. It's
algorithm and scoring scheme are designed specifically for non-coding
DNA sequence.
It uses a strategy of seeking the best possible gapless local
alignments. This happens at each step making the best possible alignment
consistent with existing alignments. It scores the significance of the
alignment based on the lengths of the aligned fragments and a background
model. These may be supplied or estimated from an auxiliary file of
intergenic DNA.
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sim4
tool for aligning cDNA and genomic DNA
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Versions of package sim4 |
Release | Version | Architectures |
bullseye | 0.0.20121010-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 0.0.20121010-1 | amd64,armel,armhf,i386 |
stretch | 0.0.20121010-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.0.20121010-5 | amd64,arm64,armhf,i386 |
sid | 0.0.20121010-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.0.20121010-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.0.20121010-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package sim4: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | comparing, searching |
works-with-format | plaintext |
|
License: DFSG free
|
sim4 is a similarity-based tool for aligning an expressed DNA sequence
(EST, cDNA, mRNA) with a genomic sequence for the gene. It also detects end
matches when the two input sequences overlap at one end (i.e., the start of
one sequence overlaps the end of the other).
sim4 employs a blast-based technique to first determine the basic matching
blocks representing the "exon cores". In this first stage, it detects all
possible exact matches of W-mers (i.e., DNA words of size W) between the two
sequences and extends them to maximal scoring gap-free segments. In the
second stage, the exon cores are extended into the adjacent as-yet-unmatched
fragments using greedy alignment algorithms, and heuristics are used to favor
configurations that conform to the splice-site recognition signals (GT-AG,
CT-AC). If necessary, the process is repeated with less stringent parameters
on the unmatched fragments.
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sim4db
batch spliced alignment of cDNA sequences to a target genome
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Versions of package sim4db |
Release | Version | Architectures |
buster | 0~20150903+r2013-6 | amd64,arm64,armhf,i386 |
sid | 0~20150903+r2013-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 0~20150903+r2013-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 0~20150903+r2013-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0~20150903+r2013-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0~20150903+r2013-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
Sim4db performs fast batch alignment of large cDNA (EST, mRNA) sequence
sets to a set of eukaryotic genomic regions. It uses the sim4 and sim4cc
algorithms to determine the alignments, but incorporates a fast sequence
indexing and retrieval mechanism, implemented in the sister package
'leaff', to speedily process large volumes of sequences.
While sim4db produces alignments in the same way as sim4 or sim4cc, it
has additional features to make it more amenable for use with whole-genome
annotation pipelines. A script file can be used to group pairings between
cDNAs and their corresponding genomic regions, to be aligned as one run
and using the same set of parameters. Sim4db also optionally reports more
than one alignment for the same cDNA within a genomic region, as long
as they meet user-defined criteria such as minimum length, percentage
sequence identity or coverage. This feature is instrumental in finding
all alignments of a gene family at one locus. Lastly, the output is
presented either as custom sim4db alignments or as GFF3 gene features.
This package is part of the Kmer suite.
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simka
comparative metagenomics method dedicated to NGS datasets
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Versions of package simka |
Release | Version | Architectures |
bookworm | 1.5.3-7 | amd64,arm64,mips64el,ppc64el |
bullseye | 1.5.3-4 | amd64,arm64,i386,ppc64el,s390x |
trixie | 1.5.3-8 | amd64,arm64,mips64el,ppc64el,riscv64 |
sid | 1.5.3-8 | amd64,arm64,mips64el,ppc64el,riscv64 |
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License: DFSG free
|
Simka is a de novo comparative metagenomics tool. Simka represents each
dataset as a k-mer spectrum and compute several classical ecological
distances between them.
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simkamin
approximate comparative metagenomics method dedicated to NGS datasets
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Versions of package simkamin |
Release | Version | Architectures |
trixie | 1.5.3-8 | all |
bookworm | 1.5.3-7 | all |
bullseye | 1.5.3-4 | all |
sid | 1.5.3-8 | all |
|
License: DFSG free
|
Simka is a de novo comparative metagenomics tool. Simka represents each
dataset as a k-mer spectrum and compute several classical ecological
distances between them.
The difference with Simka stands in the fact that SimkaMin outputs
approximate (but very similar) results by subsampling the kmer space.
With this strategy, and with default parameters, SimkaMin is an order
of magnitude faster, uses 10 times less memory and 70 times less disk
than Simka.
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ska
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Versions of package ska |
Release | Version | Architectures |
sid | 1.0+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.0+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.0+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
|
SKA (Split Kmer Analysis) is a toolkit for prokaryotic (and any other
small, haploid) DNA sequence analysis using split kmers. A split kmer is
a pair of kmers in a DNA sequence that are separated by a single base.
Split kmers allow rapid comparison and alignment of small genomes, and
is particulalry suited for surveillance or outbreak investigation. SKA
can produce split kmer files from fasta format assemblies or directly
from fastq format read sequences, cluster them, align them with or
without a reference sequence and provide various comparison and summary
statistics. Currently all testing has been carried out on high-quality
Illumina read data, so results for other platforms may vary.
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skesa
strategic Kmer extension for scrupulous assemblies
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Versions of package skesa |
Release | Version | Architectures |
trixie | 2.4.0-6 | amd64,arm64 |
bookworm | 2.4.0-6 | amd64,arm64 |
bullseye | 2.4.0-1 | amd64,i386 |
sid | 2.4.0-6 | amd64,arm64 |
|
License: DFSG free
|
SKESA is a DeBruijn graph-based de-novo assembler designed for
assembling reads of microbial genomes sequenced using Illumina.
Comparison with SPAdes and MegaHit shows that SKESA produces assemblies
that have high sequence quality and contiguity, handles low-level
contamination in reads, is fast, and produces an identical assembly for
the same input when assembled multiple times with the same or different
compute resources. SKESA has been used for assembling over 272,000 read
sets in the Sequence Read Archive at NCBI and for real-time pathogen
detection.
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skewer
post-processing of high-throughput DNA sequence reads
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Versions of package skewer |
Release | Version | Architectures |
bookworm | 0.2.2-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.2.2-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.2.2-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.2.2-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
|
skewer implements the bit-masked k-difference matching algorithm
dedicated to the task of adapter trimming and it is specially designed
for processing next-generation sequencing (NGS) paired-end sequences.
Features
- Detection and removal of adapter sequences
- Insertion and deletion allowed in pattern matching
- Targeted at Single End, Paired End (PE), and Long Mate Pair (LMP) reads
- Demultiplexing of barcoded sequencing runs
- Multi-threading support
- Trimming based on phred quality scores
- IUPAC characters for barcodes and adapters
- Compressed input and output support
The package is enhanced by the following packages:
multiqc
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smalt
Sequence Mapping and Alignment Tool
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Versions of package smalt |
Release | Version | Architectures |
stretch | 0.7.6-6 | amd64,arm64,armel,i386,mips64el,mipsel,ppc64el |
buster | 0.7.6-8 | amd64,arm64,armhf |
bullseye | 0.7.6-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.7.6-13 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.7.6-13 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.7.6-12 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 0.7.6-4 | amd64,armhf,i386 |
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License: DFSG free
|
SMALT efficiently aligns DNA sequencing reads with a reference genome.
Reads from a wide range of sequencing platforms, for example Illumina,
Roche-454, Ion Torrent, PacBio or ABI-Sanger, can be processed including
paired reads.
The software employs a perfect hash index of short words (< 20
nucleotides long), sampled at equidistant steps along the genomic
reference sequences.
For each read, potentially matching segments in the reference are
identified from seed matches in the index and subsequently aligned with
the read using a banded Smith-Waterman algorithm.
The best gapped alignments of each read is reported including a score
for the reliability of the best mapping. The user can adjust the
trade-off between sensitivity and speed by tuning the length and spacing
of the hashed words.
A mode for the detection of split (chimeric) reads is provided.
Multi-threaded program execution is supported.
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smithwaterman
determine similar regions between two strings or genomic sequences
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Versions of package smithwaterman |
Release | Version | Architectures |
stretch-backports | 0.0+git20160702.2610e25-4~bpo9+1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el |
sid | 0.0+git20160702.2610e25-12 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.0+git20160702.2610e25-12 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.0+git20160702.2610e25-12 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.0+git20160702.2610e25-11 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 0.0+20160702-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el |
buster | 0.0+git20160702.2610e25-7 | amd64,arm64,armhf,i386 |
|
License: DFSG free
|
The Smith–Waterman algorithm performs local sequence alignment; that is,
for determining similar regions between two strings or nucleotide or
protein sequences. Instead of looking at the total sequence, the
Smith–Waterman algorithm compares segments of all possible lengths and
optimizes the similarity measure.
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smrtanalysis
software suite for single molecule, real-time sequencing
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Versions of package smrtanalysis |
Release | Version | Architectures |
bookworm | 0~20210112 | all |
bullseye | 0~20210111 | all |
stretch | 0~20161126 | all |
trixie | 0~20210112 | all |
sid | 0~20210112 | all |
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License: DFSG free
|
SMRT® Analysis is a powerful, open-source bioinformatics software suite
available for analysis of DNA sequencing data from Pacific Biosciences’
SMRT technology. Users can choose from a variety of analysis protocols that
utilize PacBio® and third-party tools. Analysis protocols include de novo
genome assembly, cDNA mapping, DNA base-modification detection, and
long-amplicon analysis to determine phased consensus sequences.
This is a metapackage that depends on the components of SMRT Analysis.
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snap
location of genes from DNA sequence with hidden markov model
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Versions of package snap |
Release | Version | Architectures |
jessie | 2013-11-29-1 | amd64,armel,armhf,i386 |
sid | 2013-11-29-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 2013-11-29-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2013-11-29-11 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2013-11-29-11 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2013-11-29-9 | amd64,arm64,armhf,i386 |
stretch | 2013-11-29-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
SNAP is a general purpose gene finding program suitable for both eukaryotic
and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid
Parser.
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snap-aligner
Scalable Nucleotide Alignment Program
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Versions of package snap-aligner |
Release | Version | Architectures |
bullseye | 1.0.0+dfsg-2 | amd64,arm64,mips64el,ppc64el |
trixie | 2.0.3+dfsg-2 | amd64,arm64,mips64el,ppc64el,riscv64 |
bookworm | 2.0.2+dfsg-1 | amd64,arm64,mips64el,ppc64el |
sid | 2.0.3+dfsg-2 | amd64,arm64,mips64el,ppc64el,riscv64 |
buster | 1.0~beta.18+dfsg-3 | amd64,arm64 |
stretch | 1.0~beta.18+dfsg-1 | amd64,arm64,mips64el,ppc64el |
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License: DFSG free
|
SNAP is a new sequence aligner that is 3-20x faster and just as accurate as
existing tools like BWA-mem, Bowtie2 and Novoalign. It runs on commodity x86
processors, and supports a rich error model that lets it cheaply match reads
with more differences from the reference than other tools. This gives SNAP up
to 2x lower error rates than existing tools (in some cases) and lets it match
larger mutations that they may miss. SNAP also natively reads BAM, FASTQ, or
gzipped FASTQ, and natively writes SAM or BAM, with built-in sorting,
duplicate marking, and BAM indexing.
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sniffles
structural variation caller using third-generation sequencing
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Versions of package sniffles |
Release | Version | Architectures |
stretch | 1.0.2+ds-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.11+ds-1 | amd64,arm64,armhf,i386 |
trixie | 2.2-1 | all |
bullseye | 1.0.12b+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.2-1 | all |
bookworm | 2.0.7-1 | all |
upstream | 2.5.3 |
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License: DFSG free
|
Sniffles is a structural variation (SV) caller using third-generation
sequencing data such as those from Pacific Biosciences or Oxford
Nanopore platforms. It detects all types of SVs using evidence from
split-read alignments, high-mismatch regions, and coverage analysis.
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snippy
rapid haploid variant calling and core genome alignment
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Versions of package snippy |
Release | Version | Architectures |
sid | 4.6.0+dfsg-5 | all |
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License: DFSG free
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Snippy finds SNPs between a haploid reference genome and your NGS
sequence reads. It will find both substitutions (snps) and
insertions/deletions (indels). It will use as many CPUs as you can give
it on a single computer (tested to 64 cores). It is designed with speed
in mind, and produces a consistent set of output files in a single
folder. It can then take a set of Snippy results using the same
reference and generate a core SNP alignment (and ultimately a
phylogenomic tree).
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snp-sites
Binary code for the package snp-sites
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Versions of package snp-sites |
Release | Version | Architectures |
stretch | 2.3.2-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2.5.1-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.5.0-1 | amd64,armel,armhf,i386 |
buster | 2.4.1-1 | amd64,arm64,armhf,i386 |
bullseye | 2.5.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.5.1-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.5.1-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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This program finds single nucleotide polymorphism (SNP) sites from
multi-fasta alignment input files (which might be compressed). Its
output can be in various widely used formats (Multi Fasta Alignment,
Vcf, phylip).
The software has been developed at the Wellcome Trust Sanger Institute.
A Single Nucleotide - polymorphism (SNP, pronounced snip; plural snips)
is a DNA sequence variation occurring when a Single Nucleotide — A, T, C
or G — in the genome (or other shared sequence) differs between members
of a biological species or paired chromosomes. For example, two
sequenced DNA fragments from different individuals, AAGCCTA to AAGCTTA,
contain a difference in a single nucleotide. In this case there are two
alleles. Almost all common SNPs have only two alleles.
Topics: Genetic variation
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snpeff
genetic variant annotation and effect prediction toolbox - tool
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Versions of package snpeff |
Release | Version | Architectures |
sid | 5.2.e+dfsg-1 | all |
trixie | 5.2.e+dfsg-1 | all |
bookworm | 5.1+d+dfsg-3 | all |
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License: DFSG free
|
"We are all different!" Geneticists agree to this.
Even twins, who are said to be identical are on a molecular
level only "mostly" identical. And even within the exact same individual,
healthy cells acquire mutations such that we are all genetic mosaics.
Changes to individual cells may be induced by environmental factors,
e.g. like UV light, or happen sporadically as mishaps during cellular
divisions.
Because there are so many genetic differences, and most have just no
particular meaning for the development of a phenotype, i.e. most have no
effect, it would be nice to have heuristics implemented that direct the
researcher towards single-nucleotide polymorphisms (SNPs) that are most
likely to be relevant. This identifies the gene that causes or contributes
to, e.g, an illness, and possibly also genes that are affected by that
change. Such mechanistic understanding of a disease, particularly when
multiple genes and multiple genetic variants are contributing to the
then "polygenic" phenotype, is at the onset of drug development and
increasingly also for selecting individualized therapies in the clinic.
SnpEff is a variant annotation and effect prediction tool. It annotates
and predicts the effects of variants on genes (such as amino acid
changes).
The inputs are predicted variants (SNPs, insertions, deletions and
MNPs). The input file is usually obtained as a result of a sequencing
experiment, and it is usually in variant call format (VCF).
SnpEff analyzes the input variants. It annotates the variants and
calculates the effects they produce on known genes (e.g. amino acid
changes).
This package contains the command line tool.
The package is enhanced by the following packages:
multiqc
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snpomatic
fast, stringent short-read mapping software
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Versions of package snpomatic |
Release | Version | Architectures |
sid | 1.0-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.0-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 1.0-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.0-4 | amd64,arm64,armhf,i386 |
bullseye | 1.0-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.0-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
High throughput sequencing technologies generate large amounts of short reads.
Mapping these to a reference sequence consumes large amounts of processing
time and memory, and read mapping errors can lead to noisy or incorrect
alignments.
SNP-o-matic is a fast, stringent short-read mapping software. It supports a
multitude of output types and formats, for uses in filtering reads, alignments,
sequence-based genotyping calls, assisted reassembly of contigs etc.
Please cite:
Heinrich Magnus Manske and Dominic P. Kwiatkowski:
SNP-o-matic.
(PubMed,eprint)
Bioinformatics
25(18):2434-2435
(2009)
Topics: Genetic variation; Mapping
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snpsift
tool to annotate and manipulate genome variants - tool
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Versions of package snpsift |
Release | Version | Architectures |
trixie | 5.2.e+dfsg-1 | all |
bookworm | 5.1+dfsg2-2 | all |
sid | 5.2.e+dfsg-1 | all |
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License: DFSG free
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SnpSift is a toolbox that allows one to filter and manipulate annotated files.
Once the genomic variants have been annotated, one needs to filter them out in
order to find the "interesting / relevant variants". Given the large data
files, this is not a trivial task (e.g. one cannot load all the variants into
XLS spreadsheet). SnpSift helps to perform this VCF file manipulation and
filtering required at this stage in data processing pipelines.
This package contains the command line tool.
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soapaligner
aligner of short reads of next generation sequencers
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Versions of package soapaligner |
Release | Version | Architectures |
bookworm | 2.20-5 | amd64 |
buster | 2.20-3 | amd64 |
sid | 2.20-5 | amd64 |
trixie | 2.20-5 | amd64 |
bullseye | 2.20-5 | amd64 |
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License: DFSG free
|
This package addresses a common problem in bioinformatics that has
become routine now also in clinical research: the assembly and
comparison of the very long genomic DNA sequences from many
short reads that the machines provide.
SOAPaligner/soap2 is a member of the Short Oligonucleotide Analysis
Package (SOAP) and an updated version of SOAP software for short
oligonucleotide alignment (soap v1). The new program features in super
fast and accurate alignment for huge amounts of short reads generated by
Illumina/Solexa Genome Analyzer. Compared to soap v1, it is one order
of magnitude faster. It require only 2 minutes aligning one million
single-end reads onto the human reference genome. Another remarkable
improvement of SOAPaligner is that it now supports a wide range of the
read length.
SOAPaligner/soap2 benefitted in time and space efficiency by a revolution
in the basic data structures and algorithms used. The core algorithms and
the indexing data structures (2way-BWT) are developed by the algorithms
research group of the Department of Computer Science, the University
of Hong Kong (T.W. Lam, Alan Tam, Simon Wong, Edward Wu and S.M. Yiu).
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soapdenovo
short-read assembly method to build de novo draft assembly
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Versions of package soapdenovo |
Release | Version | Architectures |
stretch | 1.05-3 | amd64 |
trixie | 1.05-6 | amd64 |
bullseye | 1.05-6 | amd64 |
buster | 1.05-5 | amd64 |
bookworm | 1.05-6 | amd64 |
jessie | 1.05-2 | amd64 |
sid | 1.05-6 | amd64 |
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License: DFSG free
|
SOAPdenovo is a novel short-read assembly method that can build a de novo draft
assembly for the human-sized genomes. The program is specially designed to
assemble Illumina GA short reads.
It creates new opportunities for building reference
sequences and carrying out accurate analyses of unexplored genomes in a cost
effective way.
This version is not maintained anymore, consider using soapdenovo2.
Please cite:
Ruiqiang Li, Hongmei Zhu, Jue Ruan, Wubin Qian, Xiaodong Fang, Zhongbin Shi, Yingrui Li, Shengting Li, Gao Shan, Karsten Kristiansen, Songgang Li, Huanming Yang, Jian Wang and Jun Wang:
De novo assembly of human genomes with massively parallel short read sequencing.
(PubMed,eprint)
Genome Research
20(2):265-72
(2009)
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soapdenovo2
short-read assembly method to build de novo draft assembly
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Versions of package soapdenovo2 |
Release | Version | Architectures |
bookworm | 242+dfsg-3 | amd64 |
bullseye | 242+dfsg-1 | amd64 |
trixie | 242+dfsg-4 | amd64 |
buster | 241+dfsg-3 | amd64 |
sid | 242+dfsg-4 | amd64 |
jessie | 240+dfsg-2 | amd64 |
stretch | 240+dfsg1-2 | amd64 |
|
License: DFSG free
|
SOAPdenovo is a novel short-read assembly method that can build a de novo draft
assembly for the human-sized genomes. The program is specially designed to
assemble Illumina GA short reads.
It creates new opportunities for building reference
sequences and carrying out accurate analyses of unexplored genomes in a cost
effective way.
Please cite:
Ruibang Luo, Binghang Liu, Yinlong Xie, Zhenyu Li, Weihua Huang, Jianying Yuan, Guangzhu He, Yanxiang Chen, Qi Pan, Yunjie Liu, Jingbo Tang, Gengxiong Wu, Hao Zhang, Yujian Shi, Yong Liu, Chang Yu, Bo Wang, Yao Lu, Changlei Han, David W Cheung, Siu-Ming Yiu, Shaoliang Peng, Zhu Xiaoqian, Guangming Liu, Xiangke Liao, Yingrui Li, Huanming Yang, Jian Wang, Tak-Wah Lam and Jun Wang:
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler.
Giga Science
1(1):18
(2012)
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soapsnp
resequencing utility that can assemble consensus sequence of genomes
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Versions of package soapsnp |
Release | Version | Architectures |
buster | 1.03-3 | amd64,arm64,armhf,i386 |
trixie | 1.03-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.03-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.03-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.03-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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For getting ideas on the cause of diseases or their response to
therapy, and for understanding either for a particular patient,
doctors around the globe are starting to look at the genes or the
whole genome and how that sequence is different from a healthy /
well responding individual.
SOAPsnp is a member of the SOAP (Short Oligonucleotide Analysis
Package). The program is a resequencing utility. It assembles the
consensus sequence for the genome of a newly sequenced individual based
on the alignment of the raw sequencing reads on a known reference. SNPs
can then be identified on the consensus sequence through the comparison
with the reference.
SOAPsnp uses a method based on Bayes' theorem (the reverse probability
model) to call consensus genotype by carefully considering the data
quality, alignment, and recurring experimental errors. All these kinds
of information was integrated into a single quality score for each base
in PHRED scale to measure the accuracy of consensus calling. Currently,
it supports the alignment format of SOAPaligner (soap2).
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sortmerna
tool for filtering, mapping and OTU-picking NGS reads
|
Versions of package sortmerna |
Release | Version | Architectures |
stretch | 2.1-1 | amd64,i386 |
bullseye | 2.1-5 | amd64,i386 |
sid | 4.3.7-2 | amd64,i386 |
trixie | 4.3.7-2 | amd64,i386 |
buster | 2.1-3 | amd64,i386 |
bookworm | 4.3.6-2 | amd64,i386 |
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License: DFSG free
|
SortMeRNA is a biological sequence analysis tool for filtering, mapping and
OTU-picking NGS reads. The core algorithm is based on approximate seeds and
allows for fast and sensitive analyses of nucleotide sequences. The main
application of SortMeRNA is filtering rRNA from metatranscriptomic data.
Additional applications include OTU-picking and taxonomy assignation available
through QIIME v1.9+ (http://qiime.org - v1.9.0-rc1).
SortMeRNA takes as input a file of reads (fasta or fastq format) and one or
multiple rRNA database file(s), and sorts apart rRNA and rejected reads into
two files specified by the user. Optionally, it can provide high quality local
alignments of rRNA reads against the rRNA database. SortMeRNA works with
Illumina, 454, Ion Torrent and PacBio data, and can produce SAM and
BLAST-like alignments.
The package is enhanced by the following packages:
multiqc
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spaced
alignment-free sequence comparison using spaced words
|
Versions of package spaced |
Release | Version | Architectures |
bullseye | 1.2.0-201605+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.2.0-201605+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.2.0-201605+dfsg-1 | amd64,arm64,armhf,i386 |
stretch | 1.0.2+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 1.2.0-201605+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.2.0-201605+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
Spaced (Words) is a new approach to alignment-free sequence
comparison. While most alignment-free algorithms compare the
word-composition of sequences, spaced uses a pattern of care and
don't care positions. The occurrence of a spaced word in a sequence
is then defined by the characters at the match positions only, while
the characters at the don't care positions are ignored. Instead of
comparing the frequencies of contiguous words in the input sequences,
this new approach compares the frequencies of the spaced words according
to the pre-defined pattern. An information-theoretic distance measure
is then used to define pairwise distances on the set of input sequences
based on their spaced-word frequencies. Systematic test runs on real and
simulated sequence sets have shown that, for phylogeny reconstruction,
this multiple-spaced-words approach is far superior to the classical
alignment-free approach based on contiguous word frequencies.
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spades
genome assembler for single-cell and isolates data sets
|
Versions of package spades |
Release | Version | Architectures |
buster | 3.13.0+dfsg2-2 | amd64 |
stretch-backports-sloppy | 3.13.1+dfsg-2~bpo9+1 | amd64 |
stretch-backports | 3.12.0+dfsg-1~bpo9+1 | amd64 |
bullseye | 3.13.1+dfsg-2 | amd64 |
stretch | 3.9.1+dfsg-1 | amd64 |
bookworm | 3.15.5+dfsg-2 | amd64 |
trixie | 3.15.5+dfsg-8 | amd64 |
sid | 3.15.5+dfsg-8 | amd64 |
experimental | 4.0.0+dfsg1-1 | amd64 |
upstream | 4.0.0 |
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License: DFSG free
|
The SPAdes – St. Petersburg genome assembler is intended for both
standard isolates and single-cell MDA bacteria assemblies. It works
with Illumina or IonTorrent reads and is capable of providing hybrid
assemblies using PacBio and Sanger reads. You can also provide
additional contigs that will be used as long reads.
This package provides the following additional pipelines:
- metaSPAdes – a pipeline for metagenomic data sets
- plasmidSPAdes – a pipeline for extracting and assembling plasmids
from WGS data sets
- metaplasmidSPAdes – a pipeline for extracting and assembling
plasmids from metagenomic data sets
- rnaSPAdes – a de novo transcriptome assembler from RNA-Seq data
- truSPAdes – a module for TruSeq barcode assembly
- biosyntheticSPAdes – a module for biosynthetic gene cluster
assembly with paired-end reads
SPAdes provides several stand-alone binaries with relatively simple
command-line interface: k-mer counting (spades-kmercounter), assembly
graph construction (spades-gbuilder) and long read to graph aligner
(spades-gmapper).
Please cite:
Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A. Gurevich, Mikhail Dvorkin, Alexander S. Kulikov, Valery M. Lesin, Sergey I. Nikolenko, Son Pham, Andrey D. Prjibelski, Alexey V. Pyshkin, Alexander V. Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max A. Alekseyev and Pavel A. Pevzner:
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing.
(PubMed,eprint)
Journal of Computational Biology
19(5):455-477
(2012)
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|
spaln
splicing-aware transcript-alignment to genomic DNA
|
Versions of package spaln |
Release | Version | Architectures |
sid | 3.0.2+dfsg-2 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
trixie | 3.0.2+dfsg-2 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bullseye | 2.4.1+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.4.13f+dfsg-1 | amd64,arm64,mips64el,ppc64el,s390x |
upstream | 3.0.6b |
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License: DFSG free
|
Spaln (space-efficient spliced alignment) is a stand-alone program that
maps and aligns a set of cDNA or protein sequences onto a whole genomic
sequence in a single job. It also performs spliced or ordinary alignment
after rapid similarity search against a protein sequence database,
if a genomic segment or an amino acid sequence is given as a query.
spaln supports a combination of protein sequence database and a
given genomic segment and performs rapid similarity searches and
(semi-)global alignments of a set of protein sequence queries against
a protein sequence database. Spaln adopts multi-phase heuristics that
makes it possible to perform the job on a conventional personal computer.
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spoa
SIMD partial order alignment tool
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Versions of package spoa |
Release | Version | Architectures |
buster | 1.1.5-1 | amd64 |
stretch-backports-sloppy | 3.0.1-1~bpo9+1 | amd64 |
sid | 4.1.4-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 4.0.7+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 4.0.8-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch-backports | 1.1.3-2~bpo9+1 | amd64 |
trixie | 4.1.4-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
|
Spoa (SIMD POA) is a c++ implementation of the partial order alignment
(POA) algorithm (as described in 10.1093/bioinformatics/18.3.452) which
is used to generate consensus sequences (as described in
10.1093/bioinformatics/btg109). It supports three alignment modes: local
(Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment
(overlap).
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sprai
single-pass sequencing read accuracy improver
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Versions of package sprai |
Release | Version | Architectures |
buster | 0.9.9.23+dfsg-2 | amd64,arm64,armhf,i386 |
trixie | 0.9.9.23+dfsg1-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.9.9.23+dfsg1-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.9.9.23+dfsg1-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.9.9.23+dfsg1-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 0.9.9.22+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
Sprai is a tool to correct sequencing errors in single-pass reads for
de novo assembly. It is originally designed for correcting sequencing
errors in single-molecule DNA sequencing reads, especially in Continuous
Long Reads (CLRs) generated by PacBio RS sequencers. The goal of Sprai is
not maximizing the accuracy of error-corrected reads. Instead, Sprai aims
at maximizing the continuity (i.e., N50 contig length) of assembled contigs
after error correction.
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spread-phy
analyze and visualize phylogeographic reconstructions
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Versions of package spread-phy |
Release | Version | Architectures |
bookworm | 1.0.7+dfsg-5 | all |
jessie | 1.0.5+dfsg-1 (contrib) | all |
stretch | 1.0.7+dfsg-1 | all |
buster | 1.0.7+dfsg-2 | all |
bullseye | 1.0.7+dfsg-3 | all |
trixie | 1.0.7+dfsg-5 | all |
sid | 1.0.7+dfsg-5 | all |
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License: DFSG free
|
SPREAD is a user-friendly application to analyze and visualize
phylogeographic reconstructions resulting from Bayesian inference of
spatio-temporal diffusion.
There is a tutorial for SPREAD online at
http://www.kuleuven.be/aidslab/phylogeography/tutorial/spread_tutorial.html
Originally this program is named "spread". However, there is just such a
package inside Debian and thus a 'phy' for phylogeny was prepended.
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sra-toolkit
utilities for the NCBI Sequence Read Archive
|
Versions of package sra-toolkit |
Release | Version | Architectures |
jessie | 2.3.5-2+dfsg-1 | amd64,i386 |
buster | 2.9.3+dfsg-1 | amd64 |
bookworm | 3.0.3+dfsg-6~deb12u1 | amd64,arm64 |
stretch | 2.8.1-2+dfsg-2 | amd64,i386 |
trixie | 3.0.9+dfsg-7 | amd64,arm64 |
sid | 3.0.9+dfsg-7 | amd64,arm64 |
bullseye | 2.10.9+dfsg-2 | amd64 |
upstream | 3.1.1 |
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License: DFSG free
|
Tools for reading the SRA archive, generally by converting individual runs
into some commonly used format such as fastq.
The textual dumpers "sra-dump" and "vdb-dump" are provided in this
release as an aid in visual inspection. It is likely that their
actual output formatting will be changed in the near future to a
stricter, more formalized representation[s]. PLEASE DO NOT RELY UPON
THE OUTPUT FORMAT SEEN IN THIS RELEASE.
Other tools distributed in this package are:
abi-dump, abi-load
align-info
bam-load
cache-mgr
cg-load
copycat
fasterq-dump
fastq-dump, fastq-load
helicos-load
illumina-dump, illumina-load
kar
kdbmeta
latf-load
pacbio-load
prefetch
rcexplain
remote-fuser
sff-dump, sff-load
sra-pileup, sra-sort, sra-stat, srapath
srf-load
test-sra
vdb-config, vdb-copy, vdb-decrypt, vdb-encrypt, vdb-get, vdb-lock,
vdb-passwd, vdb-unlock, vdb-validate
The "help" information will be improved in near future releases, and
the tool options will become standardized across the set. More documentation
will also be provided documentation on the NCBI web site.
Tool options may change in the next release. Version 1 tool options
will remain supported wherever possible in order to preserve
operation of any existing scripts.
Please cite:
Rasko Leinonen, Ruth Akhtar, Ewan Birney, James Bonfield, Lawrence Bower, Matt Corbett, Ying Cheng, Fehmi Demiralp, Nadeem Faruque, Neil Goodgame, Richard Gibson, Gemma Hoad, Christopher Hunter, Mikyung Jang, Steven Leonard, Quan Lin, Rodrigo Lopez, Michael Maguire, Hamish McWilliam, Sheila Plaister, Rajesh Radhakrishnan, Siamak Sobhany, Guy Slater, Petra Ten Hoopen, Franck Valentin, Robert Vaughan, Vadim Zalunin, Daniel Zerbino and Guy Cochrane:
Improvements to services at the European Nucleotide Archive.
(PubMed,eprint)
Nucleic Acids Research
38(Database issue):D39-45
(2010)
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srst2
Short Read Sequence Typing for Bacterial Pathogens
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Versions of package srst2 |
Release | Version | Architectures |
bookworm | 0.2.0-9 | amd64,arm64,mips64el,ppc64el |
sid | 0.2.0-13 | amd64,arm64,mips64el,ppc64el,riscv64 |
stretch | 0.2.0-4 | amd64 |
buster | 0.2.0-6 | amd64 |
trixie | 0.2.0-13 | amd64,arm64,mips64el,ppc64el,riscv64 |
bullseye | 0.2.0-8 | amd64,arm64,mips64el,ppc64el |
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License: DFSG free
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This program is designed to take Illumina sequence data, a MLST database
and/or a database of gene sequences (e.g. resistance genes, virulence
genes, etc) and report the presence of STs and/or reference genes.
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ssake
genomics application for assembling millions of very short DNA sequences
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Versions of package ssake |
Release | Version | Architectures |
sid | 4.0.1-2 | all |
buster | 4.0-2 | all |
bullseye | 4.0-3 | all |
bookworm | 4.0.1-1 | all |
trixie | 4.0.1-2 | all |
stretch | 3.8.4-1 | all |
jessie | 3.8.2-1 | all |
Debtags of package ssake: |
biology | nuceleic-acids |
field | biology |
interface | shell |
role | program |
scope | utility |
use | analysing |
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License: DFSG free
|
The Short Sequence Assembly by K-mer search and 3′ read Extension
(SSAKE) is a genomics application for aggressively assembling
millions of short nucleotide sequences by progressively searching for
perfect 3′-most k-mers using a DNA prefix tree. SSAKE is designed to
help leverage the information from short sequences reads by
stringently clustering them into contigs that can be used to
characterize novel sequencing targets.
Topics: Sequence assembly
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sspace
scaffolding pre-assembled contigs after extension
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Versions of package sspace |
Release | Version | Architectures |
buster | 2.1.1+dfsg-4 | all |
sid | 2.1.1+dfsg-7 | all |
trixie | 2.1.1+dfsg-7 | all |
stretch | 2.1.1+dfsg-2 | all |
bookworm | 2.1.1+dfsg-7 | all |
bullseye | 2.1.1+dfsg-5 | all |
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License: DFSG free
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SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension (SSPACE)
is a script able to extend and scaffold pre-assembled contigs using one or
more mate pairs or paired-end libraries, or even a combination.
SSPACE is built based on SSAKE. Code of SSAKE is changed to be able to
extend and scaffold pre-assembled contigs for multiple paired reads
libraries.
This is the free 'basic' version of SSPACE. The non-free 'standard' version is
available directly from Baseclear.
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ssw-align
Smith-Waterman aligner based on libssw
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Versions of package ssw-align |
Release | Version | Architectures |
stretch | 1.1-1 | amd64 |
sid | 1.1-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
experimental | 1.2.5-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.1-2 | amd64 |
bullseye | 1.1-13 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.1-13 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.1-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 1.2.5 |
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License: DFSG free
|
This package provides a command-line aligner based on the libssw library,
a fast SIMD accelerated implementation of the Smith-Waterman algorithm.
The input files can be in FASTA or FASTQ format. Both target and query files
can contain multiple sequences. Each sequence in the query file will be
aligned with all sequences in the target file. Output is provided in SAM or
BLAST-like text format.
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stacks
pipeline for building loci from short-read DNA sequences
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Versions of package stacks |
Release | Version | Architectures |
stretch | 1.44-2 | amd64,arm64,armel,i386,mips64el,mipsel,ppc64el |
sid | 2.68+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.62+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.55+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.2+dfsg-1 | amd64,arm64,armhf |
trixie | 2.68+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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Stacks is a software pipeline for building loci from short-read sequences,
such as those generated on the Illumina platform. Stacks was developed to work
with restriction enzyme-based data, such as RAD-seq, for the purpose of
building genetic maps and conducting population genomics and phylogeography.
Note that this package installs Stacks such that all commands must be run as:
$ stacks
The package is enhanced by the following packages:
multiqc
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staden
DNA sequence assembly (Gap4/Gap5), editing and analysis tools
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Versions of package staden |
Release | Version | Architectures |
trixie | 2.0.0+b11-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 2.0.0+b10-1.1 | amd64,armel,armhf,i386 |
stretch | 2.0.0+b11-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.0.0+b11-4 | amd64,arm64,armhf,i386 |
bullseye | 2.0.0+b11-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.0.0+b11-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.0.0+b11-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
|
Staden is a fully developed set of DNA sequence assembly (Gap4 and
Gap5), editing and analysis tools (Spin).
Gap4 performs sequence assembly, contig ordering based on read pair
data, contig joining based on sequence comparisons, assembly checking,
repeat searching, experiment suggestion, read pair analysis and contig
editing. It has graphical views of contigs, templates, readings and
traces which all scroll in register. Contig editor searches and
experiment suggestion routines use confidence values to calculate the
confidence of the consensus sequence and hence identify only places
requiring visual trace inspection or extra data. The result is
extremely rapid finishing and a consensus of known accuracy.
Pregap4 provides a graphical user interface to set up the processing
required to prepare trace data for assembly or analysis, and automates
these processes.
Trev is a rapid and flexible viewer and editor for ABI, ALF, SCF and
ZTR trace files.
Prefinish analyses partially completed sequence assemblies and suggests
the most efficient set of experiments to help finish the project.
Tracediff and hetscan automatically locate mutations by comparing trace
data against reference traces. They annotate the mutations found ready
for viewing in gap4.
Spin analyses nucleotide sequences to find genes, restriction sites,
motifs, etc. It can perform translations, find open reading frames,
count codons, etc. Many results are presented graphically and a sliding
sequence window is linked to the graphics cursor. Spin also compares
pairs of sequences in many ways. It has very rapid dot matrix analysis,
global and local alignment algorithms, plus a sliding sequence window
linked to the graphical plots. It can compare nucleic acid against
nucleic acid, protein against protein, and protein against nucleic
acid.
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staden-io-lib-utils
programs for manipulating DNA sequencing files
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Versions of package staden-io-lib-utils |
Release | Version | Architectures |
sid | 1.15.0-1.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.14.8-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.14.11-6 | amd64,arm64,armhf,i386 |
trixie | 1.15.0-1.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.13.7-1 | amd64,armel,armhf,i386 |
bookworm | 1.14.15-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.14.13-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package staden-io-lib-utils: |
biology | nuceleic-acids, peptidic |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing |
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License: DFSG free
|
The io_lib from the Staden package is a library of file reading and writing
code to provide a general purpose trace file (and Experiment File) reading
interface. It has been compiled and tested on a variety of unix systems,
MacOS X and MS Windows.
This package contains the programs that are distributed with the Staden io_lib
for manipulating and converting sequencing data files, and in particular files
to manipulate short reads generated by second and third generation sequencers
and stored in SRF format.
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stringtie
assemble short RNAseq reads to transcripts
|
Versions of package stringtie |
Release | Version | Architectures |
bookworm | 2.2.1+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.1.4+ds-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.2.1+ds-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.2.1+ds-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 2.2.3 |
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License: DFSG free
|
The abundance of transcripts in a human tissue sample
can be determined by RNA sequencing. The exact sequence
sampled may be random, depending on the technology used.
And it may be short, i.e. shorter than the transcript.
At some point, many shorter reads need to be assembled
to the model the complete transcripts.
StringTie knows how to assemble of RNA-Seq into potential
transcripts without the need of a reference genome and
provides a quantification also of the splice variants.
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subread
toolkit for processing next-gen sequencing data
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Versions of package subread |
Release | Version | Architectures |
bullseye | 2.0.1+dfsg-1 | amd64,arm64,armel,armhf,i386,ppc64el |
stretch | 1.5.1+dfsg-4 | amd64,arm64,armel,armhf,i386,ppc64el |
bookworm | 2.0.3+dfsg-1 | amd64,arm64,armel,armhf,i386,ppc64el |
buster | 1.6.3+dfsg-1 | amd64,arm64,armhf,i386 |
sid | 2.0.7+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
trixie | 2.0.7+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
buster-backports | 2.0.0+dfsg-1~bpo10+1 | amd64,arm64,armel,armhf,i386,ppc64el |
upstream | 2.0.8 |
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License: DFSG free
|
Subread aligner can be used to align both gDNA-seq and RNA-seq reads.
Subjunc aligner was specified designed for the detection of exon-exon
junction. For the mapping of RNA-seq reads, Subread performs local
alignments and Subjunc performs global alignments.
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suitename
categorize each suite in an RNA backbone
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Versions of package suitename |
Release | Version | Architectures |
stretch | 0.3.070628-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.3.070628-2 | amd64,arm64,armhf,i386 |
sid | 0.4.130509+git20210223.ebb1325-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.4.130509+git20210223.ebb1325-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.3.070919+git20180613.ebb1325-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.4.130509+git20210223.ebb1325-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
Suitename is a program that supports the ROC RNA Ontology Consortium
consensus RNA backbone nomenclature and conformer-list development.
From dihedral-angle input for a specific RNA structure (usually from
Dangle), Suitename categorizes the RNA backbone geometry of each suite
(the sugar-to-sugar version of a residue) either as an outlier or
as belonging to one of the 53 defined conformer bins. The output is
either a one-line-per-suite report, or a linear conformer string (as
shown below the image here) in one of several variant formats. Suitename
is built into MolProbity, producing entries in the multi-criterion chart
for an RNA model and also a suitestring file.
Please cite:
Jane S. Richardson, Bohdan Schneider, Laura W. Murray, Gary J. Kapral, Robert M. Immormino, Jeffrey J. Headd, David C. Richardson, Daniela Ham, Eli Hershkovits, Loren Dean Williams, Kevin S. Keating, Anna Marie Pyle, David Micallef, John Westbrook and Helen M. Berman:
RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution).
(PubMed,eprint)
RNA
14(3):465-481
(2008)
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sumaclust
fast and exact clustering of genomic sequences
|
Versions of package sumaclust |
Release | Version | Architectures |
buster | 1.0.31-2 | amd64,arm64,armhf,i386 |
stretch | 1.0.20-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.0.36+ds-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.0.36+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.0.36+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
With the development of next-generation sequencing, efficient tools are
needed to handle millions of sequences in reasonable amounts of time.
Sumaclust is a program developed by the LECA. Sumaclust aims to cluster
sequences in a way that is fast and exact at the same time. This tool
has been developed to be adapted to the type of data generated by DNA
metabarcoding, i.e. entirely sequenced, short markers. Sumaclust
clusters sequences using the same clustering algorithm as UCLUST and CD-
HIT. This algorithm is mainly useful to detect the 'erroneous' sequences
created during amplification and sequencing protocols, deriving from
'true' sequences.
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sumatra
fast and exact comparison and clustering of sequences
|
Versions of package sumatra |
Release | Version | Architectures |
bullseye | 1.0.36+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.0.20-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.0.36+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.0.31-2 | amd64,arm64,armhf,i386 |
bookworm | 1.0.36+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
With the development of next-generation sequencing, efficient tools are
needed to handle millions of sequences in reasonable amounts of time.
Sumatra is a program developed by the LECA. Sumatra aims to compare
sequences in a way that is fast and exact at the same time. This tool
has been developed to be adapted to the type of data generated by DNA
metabarcoding, i.e. entirely sequenced, short markers. Sumatra computes
the pairwise alignment scores from one dataset or between two datasets,
with the possibility to specify a similarity threshold under which pairs
of sequences that have a lower similarity are not reported. The output
can then go through a classification process with programs such as MCL
or MOTHUR.
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sumtrees
Phylogenetic Tree Summarization and Annotation
|
Versions of package sumtrees |
Release | Version | Architectures |
sid | 4.6.1-2 | all |
bullseye | 4.5.1-1 | all |
stretch | 4.2.0+dfsg-1 | all |
trixie | 4.6.1-2 | all |
bookworm | 4.5.2-1 | all |
buster | 4.4.0-1 | all |
upstream | 5.0.1 |
|
License: DFSG free
|
SumTrees is a program to summarize non-parameteric bootstrap or
Bayesian posterior probability support for splits or clades on
phylogenetic trees.
The basis of the support assessment is typically given by a set of
non-parametric bootstrap replicate tree samples produced by programs
such as GARLI or RAxML, or by a set of MCMC tree samples produced by
programs such as Mr. Bayes or BEAST. The proportion of trees out of the
samples in which a particular split is found is taken to be the degree
of support for that split as indicated by the samples. The samples that
are the basis of the support can be distributed across multiple files,
and a burn-in option allows for an initial number of trees in each file
to be excluded from the analysis if they are not considered to be drawn
from the true support distribution.
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|
surankco
Supervised Ranking of Contigs in de novo Assemblies
|
Versions of package surankco |
Release | Version | Architectures |
bullseye | 0.0.r5+dfsg-3 | all |
buster | 0.0.r5+dfsg-2 | all |
stretch | 0.0.r5+dfsg-1 | all |
sid | 0.0.r5+dfsg-4 | all |
trixie | 0.0.r5+dfsg-4 | all |
bookworm | 0.0.r5+dfsg-3 | all |
|
License: DFSG free
|
SuRankCo is a machine learning based software to score and rank
contigs from de novo assemblies of next generation sequencing data. It
trains with alignments of contigs with known reference genomes and
predicts scores and ranking for contigs which have no related
reference genome yet.
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|
surpyvor
modification of VCF files with SURVIVOR
|
Versions of package surpyvor |
Release | Version | Architectures |
sid | 0.5-2 | all |
bookworm | 0.5-2 | all |
trixie | 0.5-2 | all |
|
License: DFSG free
|
SURVIVOR is a tool set for simulating/evaluating
structural variations, merging and comparing SVs within
and among samples, and includes various methods to
reformat or summarize structural variations.
This package provides a Python wrapper to help with its
integration in various Python-based workflows.
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survivor
tool set for simulating/evaluating SVs
|
Versions of package survivor |
Release | Version | Architectures |
bullseye | 1.0.7-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.0.7-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.0.7-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.0.7-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
SURVIVOR is a tool set for simulating/evaluating
structural variantions, merging and comparing SVs within
and among samples, and includes various methods to
reformat or summarize structural variantions.
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svim
Structural variant caller for long sequencing reads
|
Versions of package svim |
Release | Version | Architectures |
bookworm | 2.0.0-3 | all |
sid | 2.0.0-3 | all |
bullseye | 1.4.2+ds-1 | all |
trixie | 2.0.0-3 | all |
|
License: DFSG free
|
SVIM is a structural variant caller for long sequencing reads.
It is able to detect, classify and genotype five different
classes of structural variants. Unlike existing methods, SVIM
integrates information from across the genome to precisely
distinguish similar events, such as tandem and interspersed
duplications and simple insertions.
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swarm
robust and fast clustering method for amplicon-based studies
|
Versions of package swarm |
Release | Version | Architectures |
stretch | 2.1.12+dfsg-1 | amd64 |
buster | 2.2.2+dfsg-2 | amd64 |
sid | 3.1.5+dfsg-2 | amd64,arm64,ppc64el |
bullseye | 3.0.0+dfsg-2 | amd64 |
bookworm | 3.1.2+dfsg-1 | amd64,arm64,ppc64el |
trixie | 3.1.5+dfsg-2 | amd64,arm64,ppc64el |
|
License: DFSG free
|
The purpose of swarm is to provide a novel clustering algorithm to handle large
sets of amplicons. Traditional clustering algorithms results are strongly
input-order dependent, and rely on an arbitrary global clustering threshold.
swarm results are resilient to input-order changes and rely on a small local
linking threshold d, the maximum number of differences between two amplicons.
swarm forms stable high-resolution clusters, with a high yield of biological
information.
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sweed
assessment of SNPs for their evolutionary advantage
|
Versions of package sweed |
Release | Version | Architectures |
bookworm | 3.2.1+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 3.2.1+dfsg-1 | amd64,arm64,armhf,i386 |
trixie | 3.2.1+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 3.2.1+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 3.2.1+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
Biological sequences are available in ever increasing abundance across
ever larger populations for ever increasing fractions of the genome. This
tool sorts the SNPs for their active or passive contribution to a genetic
drift, i.e. to see particular sequences at a higher fraction over time.
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t-coffee
Multiple Sequence Alignment
|
Versions of package t-coffee |
Release | Version | Architectures |
buster | 12.00.7fb08c2-4 | amd64,arm64,armhf,i386 |
trixie | 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 13.41.0.28bdc39+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 11.00.8cbe486-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 11.00.8cbe486-1 | amd64,armel,armhf,i386 |
Debtags of package t-coffee: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing, comparing |
works-with-format | plaintext |
|
License: DFSG free
|
T-Coffee is a multiple sequence alignment package. Given a set of
sequences (Proteins or DNA), T-Coffee generates a multiple sequence
alignment. Version 2.00 and higher can mix sequences and structures.
T-Coffee allows the combination of a collection of multiple/pairwise,
global or local alignments into a single model. It can also
estimate the level of consistency of each position within the new
alignment with the rest of the alignments. See the pre-print for more
information
T-Coffee has a special called M-Coffee that makes it possible to combine the
output of many multiple sequence alignment packages. In its published version,
it uses MUSCLE, PROBCONS, POA, DiAlign-TS, MAFFT, Clustal W, PCMA and
T-Coffee. A special version has been made for Debian, DM-Coffee, that uses
only free software by replacing Clustal W by Kalign. Using the 8 Methods of
M-Coffee can sometimes be a bit heavy. You can use a subset of your favorite
methods if you prefer.
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tabix
generic indexer for TAB-delimited genome position files
|
Versions of package tabix |
Release | Version | Architectures |
jessie | 0.2.6-2 | armhf |
bullseye | 1.11-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.9-12~deb10u1 | amd64,arm64,armhf,i386 |
stretch-backports | 1.7-2~bpo9+1 | amd64,arm64,armel,armhf,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.1-1 | amd64,armel,i386 |
stretch | 1.3.2-2 | amd64,arm64,armel,i386,mips64el,mipsel,ppc64el |
bookworm | 1.16+ds-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.20+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.20+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
experimental | 1.21+ds-0+exp2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 1.21 |
Debtags of package tabix: |
role | program |
works-with-format | html |
|
License: DFSG free
|
Tabix indexes files where some columns indicate sequence coordinates: name
(usually a chromosome), start and stop. The input data file must be position
sorted and compressed by bgzip (provided in this package), which has a gzip
like interface. After indexing, tabix is able to quickly retrieve data lines by
chromosomal coordinates. Fast data retrieval also works over network if an URI
is given as a file name.
This package is built from the HTSlib source, and provides the bgzip, htsfile,
and tabix tools.
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tantan
low complexity and tandem repeat masker for biosequences
|
Versions of package tantan |
Release | Version | Architectures |
trixie | 51-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 13-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 23-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 22-1 | amd64,arm64,armhf,i386 |
sid | 51-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 40-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
tantan is a tool to mask simple regions (low complexity and short-period tandem
repeats) in DNA, RNA, and protein sequences. The aim of tantan is to prevent
false predictions when searching for homologous regions between two sequences.
Simple repeats often align strongly to each other, causing false homology
predictions.
Topics: Sequence composition, complexity and repeats
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terraphast
enumerate terraces in phylogenetic tree space
|
Versions of package terraphast |
Release | Version | Architectures |
bookworm | 0.0+git20200413.8af2e4c+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.0+git20200413.8af2e4c+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.0+git20200413.8af2e4c+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
Terraphast takes a .nkw file in Newick format and a genes/sites file,
which denotes whether (1) or not (0) gene i is present in species j.
Program output states some imput data properties, the species whose leaf
edge is used as a new tree root, and the resulting supertree in
compressed newick format.
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theseus
superimpose macromolecules using maximum likelihood
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Versions of package theseus |
Release | Version | Architectures |
bookworm | 3.3.0-14 | amd64,i386 |
buster | 3.3.0-8 | amd64,arm64,armhf,i386 |
stretch | 3.3.0-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 3.0.0-1 | amd64,armel,armhf,i386 |
sid | 3.3.0-14 | amd64,i386 |
trixie | 3.3.0-14 | amd64,i386 |
bullseye | 3.3.0-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package theseus: |
biology | peptidic |
field | biology, biology:bioinformatics, biology:structural |
interface | commandline |
role | program |
use | analysing, comparing |
works-with-format | plaintext |
|
License: DFSG free
|
Theseus is a program that simultaneously superimposes multiple
macromolecular structures. Theseus finds the optimal solution to the
superposition problem using the method of maximum likelihood. By
down-weighting variable regions of the superposition and by correcting for
correlations among atoms, the ML superposition method produces very
accurate structural alignments.
When macromolecules with different residue sequences are superimposed,
other programs and algorithms discard residues that are aligned with
gaps. Theseus, however, uses a novel superimposition algorithm that
includes all of the data.
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thesias
Testing Haplotype Effects In Association Studies
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Versions of package thesias |
Release | Version | Architectures |
bookworm | 3.1.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster-backports | 3.1.1-1~bpo10+1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 3.1.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 3.1.1-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 3.1.1-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
The objectif of the THESIAS program is to performed haplotype-based
association analysis in unrelated individuals. This program is based
on the maximum likelihood model described in Tregouet et al. 2002
(Hum Mol Genet 2002,11: 2015-2023) and is linked to the SEM algorithm
(Tregouet et al. Ann Hum Genet 2004,68: 165-177).
THESIAS allows one to simultaneous estimate haplotype frequencies
and their associate effects on the phenotype of interest.
In this new THESIAS release, quantitative, qualitative (logistic
and matched-pair analysis), categorical and survival outcomes can be
studied. X-linked haplotype analysis is also feasible.
Covariate-adjusted haplotype effects as well as haplotype x covariate
interactions can also be investigated.
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tiddit
structural variant calling
|
Versions of package tiddit |
Release | Version | Architectures |
sid | 3.6.1+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
bookworm | 3.5.2+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
trixie | 3.6.1+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
bullseye | 2.12.0+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 3.9.0 |
|
License: DFSG free
|
TIDDIT is a tool to used to identify chromosomal rearrangements using
Mate Pair or Paired End sequencing data. TIDDIT identifies intra and inter-
chromosomal translocations, deletions, tandem-duplications and
inversions, using supplementary alignments as well as discordant pairs.
TIDDIT has two analysis modules. The sv mode, which is used to search
for structural variants. And the cov mode that analyse the read depth of
a bam file and generates a coverage report.
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tigr-glimmer
Gene detection in archea and bacteria
|
Versions of package tigr-glimmer |
Release | Version | Architectures |
bookworm | 3.02b-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 3.02b-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 3.02b-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 3.02b-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 3.02b-2 | amd64,arm64,armhf,i386 |
jessie | 3.02-3 | amd64,armel,armhf,i386 |
stretch | 3.02b-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package tigr-glimmer: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | searching |
works-with-format | plaintext |
|
License: DFSG free
|
Developed by the TIGR institute this software detects coding sequences in
bacteria and archea.
Glimmer is a system for finding genes in microbial DNA, especially the
genomes of bacteria and archaea. Glimmer (Gene Locator and Interpolated
Markov Modeler) uses interpolated Markov models (IMMs) to identify the
coding regions and distinguish them from noncoding DNA.
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tipp
tool for Taxonomic Identification and Phylogenetic Profiling
|
Versions of package tipp |
Release | Version | Architectures |
sid | 1.0+dfsg-3 | amd64,arm64 |
|
License: DFSG free
|
TIPP is a modification of SEPP for classifying query sequences (i.e. reads)
using phylogenetic placement.
TIPP inserts each read into a taxonomic tree and uses the insertion location
to identify the taxonomic lineage of the read. The novel idea behind TIPP is
that rather than using the single best alignment and placement for taxonomic
identification, it uses a collection of alignments and placements and
considers statistical support for each alignment and placement.
TIPP can also be used for abundance estimation by computing an abundance
profile on the reads binned to marker genes in a reference dataset.
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tm-align
structural alignment of proteins
|
Versions of package tm-align |
Release | Version | Architectures |
stretch | 20160521+dfsg-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 20190822+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 20190822+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 20190822+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 20190822+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 20170708+dfsg-2 | amd64,arm64,armhf,i386 |
jessie | 20140601+dfsg-1 | amd64,armel,armhf,i386 |
Debtags of package tm-align: |
role | program |
|
License: DFSG free
|
TM-align is a computer algorithm for protein structure alignment using
dynamic programming. The scoring is performed by the TM-score rotation
matrix. This is similar to the RMSD in that unaligned portions of the
structure influence the scoring less than the more structurally conserved
regions.
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tnseq-transit
statistical calculations of essentiality of genes or genomic regions
|
Versions of package tnseq-transit |
Release | Version | Architectures |
stretch-backports | 2.2.1-2~bpo9+1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 3.2.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.3.4-1 | amd64 |
sid | 3.3.4-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 3.2.7-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 3.3.4-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 3.3.12 |
|
License: DFSG free
|
This is a software that can be used to analyze Tn-Seq datasets. It
includes various statistical calculations of essentiality of genes or
genomic regions (including conditional essentiality between 2
conditions). These methods were developed and tested as a collaboration
between the Sassetti lab (UMass) and the Ioerger lab (Texas A&M)
TRANSIT is capable of analyzing TnSeq libraries constructed with Himar1
or Tn5 datasets.
TRANSIT assumes you have already done pre-processing of raw sequencing
files (.fastq) and extracted read counts into a .wig formatted file.
The .wig file should contain the counts at all sites where an insertion
could take place (including sites with no reads). For Himar1 datasets
this is all TA sites in the genome. For Tn5 datasets this would be all
nucleotides in the genome.
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toil
cross-platform workflow engine
|
Versions of package toil |
Release | Version | Architectures |
bullseye | 5.2.0-5 | all |
sid | 6.1.0-4 | all |
bookworm | 5.9.2-2+deb12u1 | all |
buster | 3.18.0-2 | all |
upstream | 7.0.0 |
|
License: DFSG free
|
Toil is a scalable, efficient, cross-platform and easy-to-use workflow
engine in pure Python. It works with several well established load
balancers like Slurm or the Sun Grid Engine. Toil is also compatible with
the Common Workflow Language (CWL) via the "toil-cwl-runner" interface, which
this package make available via the Debian alternativess system under the
alias "cwl-runner".
Please cite:
John Vivian, Arjun Arkal Rao, Frank Austin Nothaft, Christopher Ketchum, Joel Armstrong, Adam Novak, Jacob Pfeil, Jake Narkizian Alden D. Deran, Audrey Musselman-Brown, Hannes Schmidt, Peter Amstutz, Brian Craft, Mary Goldman, Kate Rosenbloom, Melissa Cline, Brian O'Connor, Megan Hanna, Chet Birger, W. James Kent David A. Patterson, Anthony D. Joseph, Jingchun Zhu, Sasha Zaranek, Gad Getz, David Haussler and Benedict Paten:
Toil enables reproducible, open source, big biomedical data analyses.
Nature Biotechnology
35(4):314–316
(2017)
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tombo
identification of modified nucleotides from raw nanopore sequencing data
|
Versions of package tombo |
Release | Version | Architectures |
trixie | 1.5.1-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.5.1-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.5.1-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.5.1-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
Tombo is a suite of tools primarily for the identification of modified
nucleotides from nanopore sequencing data. Tombo also provides tools for
the analysis and visualization of raw nanopore signal.
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tophat
fast splice junction mapper for RNA-Seq reads
|
Versions of package tophat |
Release | Version | Architectures |
stretch | 2.1.1+dfsg-2 | amd64 |
buster | 2.1.1+dfsg1-2 | amd64,arm64 |
jessie | 2.0.13+dfsg-1 | amd64 |
|
License: DFSG free
|
TopHat aligns RNA-Seq reads to mammalian-sized genomes using the ultra
high-throughput short read aligner Bowtie, and then analyzes the
mapping results to identify splice junctions between exons.
TopHat is a collaborative effort between the University of Maryland
Center for Bioinformatics and Computational Biology and the
University of California, Berkeley Departments of Mathematics and
Molecular and Cell Biology.
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tophat-recondition
post-processor for TopHat unmapped reads
|
Versions of package tophat-recondition |
Release | Version | Architectures |
bullseye | 1.4-3 | all |
trixie | 1.4-3 | all |
sid | 1.4-3 | all |
bookworm | 1.4-3 | all |
|
License: DFSG free
|
tophat-recondition is a post-processor for TopHat unmapped reads
(contained in unmapped.bam), making them compatible with downstream
tools (e.g., the Picard suite, samtools, GATK) (TopHat issue #17). It
also works around bugs in TopHat:
- the "mate is unmapped" SAM flag is not set on any reads in the
unmapped.bam file (TopHat issue #3)
- the mapped mate of an unmapped read can be absent from
accepted_hits.bam, creating a mismatch between the file and the unmapped
read's flags (TopHat issue #16)
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topp
set of programs implementing The OpenMS Proteomic Pipeline
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Versions of package topp |
Release | Version | Architectures |
bookworm | 2.6.0+cleaned1-3 | amd64,arm64,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.6.0+cleaned1-4 | amd64,arm64,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.6.0+cleaned1-4 | amd64,arm64,i386,mips64el,ppc64el,riscv64,s390x |
buster | 2.4.0-real-1 | amd64,arm64,i386 |
jessie | 1.11.1-5 | amd64,armel,armhf,i386 |
bullseye | 2.6.0+cleaned1-3 | amd64,arm64,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package topp: |
uitoolkit | qt |
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License: DFSG free
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TOPP (the OpenMS proteomic pipeline) is a pipeline for the analysis
of HPLC/MS data. It consists of a set of numerous small applications
that can be chained together to create analysis pipelines tailored
for a specific problem. The applications make use of the libopenms
library. Some examples of these applications are :
- TOPPView: A viewer for mass spectrometry data.
- TOPPAS: An assistant for GUI-driven TOPP workflow design.
- DTAExtractor: Extracts spectra of an MS run file to several
files in DTA format.
- FileConverter: Converts between different MS file formats.
- FileFilter: Extracts or manipulates portions of data from peak,
feature or consensus feature files.
- SpectraMerger: Merges spectra from an LC/MS map, either by
precursor or by RT blocks.
- BaselineFilter: Removes the baseline from profile spectra using a
top-hat filter.
- InternalCalibration: Applies an internal calibration.
- PTModel: Trains a model for the prediction of proteotypic
peptides from a training set.
- RTPredict: Predicts retention times for peptides using a model
trained by RTModel.
- ExecutePipeline: Executes workflows created by TOPPAS.
Please cite:
Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert and Oliver Kohlbacher:
OpenMS – an Open-Source Software Framework for Mass Spectrometry.
(PubMed,eprint)
BMC Bioinformatics
9(163)
(2008)
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toppred
transmembrane topology prediction
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Versions of package toppred |
Release | Version | Architectures |
buster | 1.10-7 | amd64,arm64,armhf,i386 |
stretch | 1.10-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 1.10-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.10-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.10-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.10-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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Toppred is a program to determine the topology of a transmembrane
protein based on G. von Heijne algorithm.
Each sequence from seq data in fasta format is processed, and toppred
generate the Hydrophobycity profile of the sequence, and the
corresponding hydrophobycities values in the file sequence-ID.hydro.
Furthermore, the predicted topologies are represented as png images.
Each topology is stored in file sequence-ID-number.png
The hydrophobicity profile is computed using a window formed by a core
rectangular window of size n, flanked by 2 triangular windows of size q.
NB rectangular and triangular mean that the ponderation values inside
those windows are respectively constant and variable.
This program is a new implementation of the original toppred program,
based on G. von Heijne algorithm
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tortoize
Application to calculate ramachandran z-scores
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Versions of package tortoize |
Release | Version | Architectures |
bullseye | 2.0.1-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.0.11-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.0.11-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.0.13-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
sid | 2.0.11-1 | s390x |
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License: DFSG free
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Tortoize validates protein structure models by checking the
Ramachandran plot and side-chain rotamer distributions. Quality
Z-scores are given at the residue level and at the model level
(ramachandran-z and torsions-z). Higher scores are better. To compare
models or to describe the reliability of the model Z-scores jackknife-
based standard deviations are also reported (ramachandran-jackknife-sd
and torsion-jackknife-sd).
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trace2dbest
bulk submission of chromatogram data to dbEST
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Versions of package trace2dbest |
Release | Version | Architectures |
trixie | 3.0.1-2 | all |
buster | 3.0.1-1 | all |
bullseye | 3.0.1-2 | all |
bookworm | 3.0.1-2 | all |
sid | 3.0.1-2 | all |
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License: DFSG free
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ESTs are short sequences derived from reverse-transcribed RNA.
Their abundances yield insights in the expression of genes across
tissues, support the discovery of new genes and allow one to assess
the coverage of whole genome sequencing projects. Public databases
like dbEST at the NCBI collect this data.
trace2dbEST process raw sequenceing chromatograph trace files from
EST projects into quality-checked sequences, ready for submission to
dbEST. trace2dbEST guides you through the creation of all the necessary
files for submission of ESTs to dbEST. trace2dbest makes use of other
software (available free under academic licence) that you will need to
have installed, namely phred, cross_match and (optionally) BLAST.
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tracetuner
interpretation of DNA Sanger sequencing data
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Versions of package tracetuner |
Release | Version | Architectures |
buster | 3.0.6~beta+dfsg-1 | amd64,arm64,armhf,i386 |
sid | 3.0.6~beta+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 3.0.6~beta+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 3.0.6~beta+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.0.6~beta+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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Tracetuner is a tool for base and quality calling of trace files from
DNA sequencing instruments.
Traditional DNA sequencing yields curves from four different
channels or light frequencies that human or (preferably) machines
are interpreting to determine the actual base (A,C,G or T) and
the confidence with which this is determined.
TraceTuner is a DNA sequencing quality value, base calling and trace
processing software application originally developed by Paracel,
Inc. While providing a flexible interface and capability to adopt
the "pure" base calls produced by Phred, KB or any other "original"
caller, it offers competitive features not currently available in other
tools, such as customized calibration of quality values, advanced
heterozygote and mixed base calling and deconvolving the "mixed"
electropherograms resulting from the presence of indels into a couple of
"pure" electropherograms.
Later versions
Previous versions of TraceTuner were used by
Celera Genomics to process over 27 million reads from both Drosophila
and human genome projects.
In 2000, Applied Biosystems
bundled TraceTuner with ABI3700 Genome Analyzers and shipped it to the
customers of these capillary electrophoresis sequencers.
its SNP detection and genotyping software product SeqScape.
TraceTuner implements an advanced peak processing technology for resolving
overlapping peaks of the same dye color into individual, or "intrinsic"
peaks. TraceTuner, for its support of mixed base calling, have been used by
the research community, the private biotech sector, and the U.S. government
as components of different variant detection, genotyping and forensic
software applications (e.g. Applied Biosystems SeqScape, Paracel Genome
Assembler, MTexpert, etc.).
This technology was protected by US Patent #6,681,186. Currently,
TraceTuner is an open source software, which has been used by J. Craig
Venter Institute's DNA Sequencing and Resequencing pipelines.
This package prepares an important piece of human history to be used
with new data on new machines or to revisit older observations..
Please cite:
G.A.Denisov, A.B.Arehart and M.D.Curtin:
A system and method for improving the accuracy of DNA sequencing and error probability estimation through application of a mathematical model to the analysis of electropherograms. US Patent 6681186.
(2004)
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transdecoder
find coding regions within RNA transcript sequences
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Versions of package transdecoder |
Release | Version | Architectures |
stretch | 3.0.1+dfsg-1 | all |
bullseye | 5.0.1-3 | all |
sid | 5.7.1-2 | all |
trixie | 5.7.1-2 | all |
buster | 5.0.1-2 | all |
bookworm | 5.0.1-5 | all |
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License: DFSG free
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TransDecoder identifies candidate coding regions within transcript sequences,
such as those generated by de novo RNA-Seq transcript assembly using Trinity,
or constructed based on RNA-Seq alignments to the genome using Tophat and
Cufflinks.
TransDecoder identifies likely coding sequences based on the following
criteria:
- a minimum length open reading frame (ORF) is found in a transcript sequence
- a log-likelihood score similar to what is computed by the GeneID software
is > 0.
- the above coding score is greatest when the ORF is scored in the 1st
reading frame as compared to scores in the other 5 reading frames.
- if a candidate ORF is found fully encapsulated by the coordinates of
another candidate ORF, the longer one is reported. However, a single
transcript can report multiple ORFs (allowing for operons, chimeras, etc).
- optional the putative peptide has a match to a Pfam domain above the noise
cutoff score.
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transrate-tools
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Versions of package transrate-tools |
Release | Version | Architectures |
bookworm | 1.0.0-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.0.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.0-2 | amd64,arm64,armhf,i386 |
bullseye | 1.0.0-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.0.0-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.0.0-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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Transrate is a library and command-line tool for quality assessment of de-novo
transcriptome assemblies.
This package provides command line tools used by transrate to process BAM
files.
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transtermhp
find rho-independent transcription terminators in bacterial genomes
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Versions of package transtermhp |
Release | Version | Architectures |
buster | 2.09-4 | amd64,arm64,armhf,i386 |
jessie | 2.09-2 | amd64,armel,armhf,i386 |
sid | 2.09-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 2.09-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 2.09-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.09-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.09-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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TransTermHP finds rho-independent transcription terminators in
bacterial genomes. Each terminator found by the program is assigned a
confidence value that estimates its probability of being a true
terminator. TransTermHP is the successor of TransTerm which was using
very different search and scoring algorithms.
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tree-ppuzzle
Parallelized reconstruction of phylogenetic trees by maximum likelihood
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Versions of package tree-ppuzzle |
Release | Version | Architectures |
buster | 5.2-11 | amd64,arm64,armhf,i386 |
jessie | 5.2-7 | amd64,armel,armhf,i386 |
sid | 5.3~rc16+dfsg-12 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 5.2-8 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 5.3~rc16+dfsg-12 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 5.3~rc16+dfsg-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 5.3~rc16+dfsg-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package tree-ppuzzle: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing, comparing |
works-with-format | plaintext |
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License: DFSG free
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TREE-PUZZLE (the new name for PUZZLE) is an interactive console program that
implements a fast tree search algorithm, quartet puzzling, that allows
analysis of large data sets and automatically assigns estimations of support
to each internal branch. TREE-PUZZLE also computes pairwise maximum
likelihood distances as well as branch lengths for user specified trees.
Branch lengths can also be calculated under the clock-assumption. In
addition, TREE-PUZZLE offers a novel method, likelihood mapping, to
investigate the support of a hypothesized internal branch without
computing an overall tree and to visualize the phylogenetic content of
a sequence alignment.
This is the parallelized version of tree-puzzle.
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tree-puzzle
Reconstruction of phylogenetic trees by maximum likelihood
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Versions of package tree-puzzle |
Release | Version | Architectures |
sid | 5.3~rc16+dfsg-12 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 5.2-7 | amd64,armel,armhf,i386 |
stretch | 5.2-8 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 5.2-11 | amd64,arm64,armhf,i386 |
bullseye | 5.3~rc16+dfsg-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 5.3~rc16+dfsg-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 5.3~rc16+dfsg-12 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package tree-puzzle: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing, comparing |
works-with-format | plaintext |
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License: DFSG free
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TREE-PUZZLE (the new name for PUZZLE) is an interactive console program that
implements a fast tree search algorithm, quartet puzzling, that allows
analysis of large data sets and automatically assigns estimations of support
to each internal branch. TREE-PUZZLE also computes pairwise maximum
likelihood distances as well as branch lengths for user specified trees.
Branch lengths can also be calculated under the clock-assumption. In
addition, TREE-PUZZLE offers a novel method, likelihood mapping, to
investigate the support of a hypothesized internal branch without
computing an overall tree and to visualize the phylogenetic content of
a sequence alignment.
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treeview
Java re-implementation of Michael Eisen's TreeView
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Versions of package treeview |
Release | Version | Architectures |
stretch | 1.1.6.4+dfsg1-2 | all |
buster | 1.1.6.4+dfsg1-4 | all |
bullseye | 1.2.0+dfsg-1 | all |
bookworm | 1.2.0+dfsg-1 | all |
trixie | 1.2.0+dfsg-2 | all |
sid | 1.2.0+dfsg-2 | all |
jessie | 1.1.6.4+dfsg-1 (contrib) | all |
upstream | 1.2.1 |
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License: DFSG free
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TreeView creates a matrix-like display of expression data, known as
Eisen clustering. The original implementation was a Windows program
named TreeView by Michael Eisen. This TreeView package, sometimes also
referred to as jTreeView, was rewritten in Java under a free license.
Java TreeView is an extensible viewer for microarray data in
PCL or CDT format.
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treeviewx
Displays and prints phylogenetic trees
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Versions of package treeviewx |
Release | Version | Architectures |
bookworm | 0.5.1+git20100823.7e4d0e9-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.5.1+git20100823.7e4d0e9-1 | amd64,arm64,armhf,i386 |
trixie | 0.5.1+git20100823.7e4d0e9-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.5.1+git20100823.7e4d0e9-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 0.5.1+20100823-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0.5.1+20100823-3 | amd64,armel,armhf,i386 |
bullseye | 0.5.1+git20100823.7e4d0e9-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package treeviewx: |
field | biology, biology:bioinformatics |
interface | x11 |
role | program |
scope | utility |
uitoolkit | wxwidgets |
use | viewing |
works-with-format | pdf, plaintext, postscript, svg |
x11 | application |
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License: DFSG free
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TreeView X is an open source and multi-platform program to display
phylogenetic trees. It can read and display NEXUS and Newick format tree files
(such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs). It
allows one to order the branches of the trees, and to export the trees in SVG
format.
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trf
locate and display tandem repeats in DNA sequences
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Versions of package trf |
Release | Version | Architectures |
bullseye | 4.09.1-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 4.09.1-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 4.09.1-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 4.09.1-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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A tandem repeat in DNA is two or more adjacent, approximate copies of a
pattern of nucleotides. Tandem Repeats Finder is a program to locate and
display tandem repeats in DNA sequences. In order to use the program,
the user submits a sequence in FASTA format. There is no need to specify
the pattern, the size of the pattern or any other parameter. The output
consists of two files: a repeat table file and an alignment file. The
repeat table, viewable in a web browser, contains information about each
repeat, including its location, size, number of copies and nucleotide
content. Clicking on the location indices for one of the table entries
opens a second browser page that shows an alignment of the copies
against a consensus pattern. The program is very fast, analyzing
sequences on the order of .5Mb in just a few seconds. Submitted
sequences may be of arbitrary length. Repeats with pattern size in the
range from 1 to 2000 bases are detected.
The package is enhanced by the following packages:
trf-examples
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trim-galore
automate quality and adapter trimming for DNA sequencing
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Versions of package trim-galore |
Release | Version | Architectures |
trixie | 0.6.10-1 | all |
sid | 0.6.10-1 | all |
bookworm | 0.6.10-1 | all |
bullseye | 0.6.6-1 | all |
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License: DFSG free
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Trim Galore! is a wrapper script to automate quality and adapter trimming
as well as quality control, with some added functionality to remove
biased methylation positions for RRBS sequence files (for directional,
non-directional (or paired-end) sequencing). It's main features are:
- For adapter trimming, Trim Galore! uses the first 13 bp of Illumina
standard adapters ('AGATCGGAAGAGC') by default (suitable for both ends
of paired-end libraries), but accepts other adapter sequence, too
- For MspI-digested RRBS libraries, Trim Galore! performs quality and
adapter trimming in two subsequent steps. This allows it to remove
2 additional bases that contain a cytosine which was artificially
introduced in the end-repair step during the library preparation
- For any kind of FastQ file other than MspI-digested RRBS, Trim
Galore! can perform single-pass adapter- and quality trimming
- The Phred quality of basecalls and the stringency for adapter removal
can be specified individually
- Trim Galore! can remove sequences if they become too short during
the trimming process. For paired-end files Trim Galore! removes entire
sequence pairs if one (or both) of the two reads became shorter than
the set length cutoff. Reads of a read-pair that are longer than a
given threshold but for which the partner read has become too short
can optionally be written out to single-end files. This ensures that
the information of a read pair is not lost entirely if only one read
is of good quality
- Trim Galore! can trim paired-end files by 1 additional bp from the 3'
end of all reads to avoid problems with invalid alignments with Bowtie 1
- Trim Galore! accepts and produces standard or gzip compressed FastQ files
- FastQC can optionally be run on the resulting output files once
trimming has completed
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trimmomatic
flexible read trimming tool for Illumina NGS data
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Versions of package trimmomatic |
Release | Version | Architectures |
sid | 0.39+dfsg-2 | all |
bookworm | 0.39+dfsg-2 | all |
jessie | 0.32+dfsg-4 | all |
stretch | 0.36+dfsg-1 | all |
trixie | 0.39+dfsg-2 | all |
buster | 0.38+dfsg-1 | all |
bullseye | 0.39+dfsg-2 | all |
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License: DFSG free
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Trimmomatic performs a variety of useful trimming tasks for illumina
paired-end and single ended data.The selection of trimming steps and
their associated parameters are supplied on the command line.
The current trimming steps are:
- ILLUMINACLIP: Cut adapter and other illumina-specific sequences from
the read.
- SLIDINGWINDOW: Perform a sliding window trimming, cutting once thes
average quality within the window falls below a threshold.
- LEADING: Cut bases off the start of a read, if below a threshold quality
- TRAILING: Cut bases off the end of a read, if below a threshold quality
- CROP: Cut the read to a specified length
- HEADCROP: Cut the specified number of bases from the start of the read
- MINLENGTH: Drop the read if it is below a specified length
- TOPHRED33: Convert quality scores to Phred-33
- TOPHRED64: Convert quality scores to Phred-64
It works with FASTQ (using phred + 33 or phred + 64 quality scores,
depending on the Illumina pipeline used), either uncompressed or
gzipp'ed FASTQ. Use of gzip format is determined based on the .gz
extension.
The package is enhanced by the following packages:
multiqc
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trinityrnaseq
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Versions of package trinityrnaseq |
Release | Version | Architectures |
sid | 2.15.2+dfsg-1 | amd64,arm64,ppc64el,riscv64 |
bullseye | 2.11.0+dfsg-6 | amd64,arm64 |
buster | 2.6.6+dfsg-6 | amd64 |
trixie | 2.15.2+dfsg-1 | amd64,arm64,ppc64el,riscv64 |
stretch | 2.2.0+dfsg-2 | amd64 |
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License: DFSG free
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Trinity represents a novel method for the efficient and robust de novo
reconstruction of transcriptomes from RNA-seq data. Trinity combines three
independent software modules: Inchworm, Chrysalis, and Butterfly, applied
sequentially to process large volumes of RNA-seq reads. Trinity partitions
the sequence data into many individual de Bruijn graphs, each representing the
transcriptional complexity at a given gene or locus, and then processes
each graph independently to extract full-length splicing isoforms and to tease
apart transcripts derived from paralogous genes.
Please cite:
Manfred G Grabherr, Brian J Haas, Moran Yassour, Joshua Z Levin, Dawn A Thompson, Ido Amit, Xian Adiconis, Lin Fan, Raktima Raychowdhury, Qiandong Zeng, Zehua Chen, Evan Mauceli, Nir Hacohen, Andreas Gnirke, Nicholas Rhind, Federica di Palma, Bruce W Birren, Chad Nusbaum, Kerstin Lindblad-Toh, Nir Friedman and Aviv Regev:
Full-length transcriptome assembly from RNA-Seq data without a reference genome..
(PubMed)
Nature Biotechnology
29(7):644-652
(2011)
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tvc
genetic variant caller for Ion Torrent sequencing platforms
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Versions of package tvc |
Release | Version | Architectures |
buster | 5.0.3+git20151221.80e144e+dfsg-2 | amd64,arm64,armhf,i386 |
bookworm | 5.0.3+git20151221.80e144e+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 5.0.3+git20151221.80e144e+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 5.0.3+git20151221.80e144e+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 5.0.3+git20151221.80e144e+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
Torrent Variant Caller (TVC) is a genetic variant caller for
Ion Torrent sequencing platforms, and is specially optimized to exploit the
underlying flow signal information in the statistical model
to evaluate variants. Torrent Variant Caller is designed to call
single-nucleotide polymorphisms (SNPs), multi-nucleotide polymorphisms (MNPs),
insertions, deletions, and block substitutions.
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twopaco
build the compacted de Bruijn graph from many complete genomes
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Versions of package twopaco |
Release | Version | Architectures |
trixie | 1.0.0+dfsg-1 | amd64,arm64,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.0.0+dfsg-1 | amd64,arm64,armhf,i386,mips64el,ppc64el,s390x |
sid | 1.0.0+dfsg-1 | amd64,arm64,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
TwoPaCo is an implementation of the algorithm described in the paper
"TwoPaCo: An efficient algorithm to build the compacted de Bruijn graph
from many complete genomes".
This package contains two programs:
twopaco: tool for direct construction of the compressed graph from
multiple complete genomes
graphdump: utility that turns output of twopaco into a text format
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uc-echo
error correction algorithm designed for short-reads from NGS
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Versions of package uc-echo |
Release | Version | Architectures |
jessie | 1.12-7 | amd64,armel,armhf,i386 |
stretch | 1.12-9 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 1.12-19 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.12-11 | amd64,arm64,armhf,i386 |
bookworm | 1.12-18 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.12-15 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.12-19 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
|
ECHO is an error correction algorithm designed for short-reads
from next-generation sequencing platforms such as Illumina's
Genome Analyzer II. The algorithm uses a Bayesian framework to
improve the quality of the reads in a given data set by employing
maximum a posteriori estimation.
Topics: Data management; Sequencing
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ugene
integrated bioinformatics toolkit
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Versions of package ugene |
Release | Version | Architectures |
buster-backports | 33.0+dfsg-1~bpo10+1 (non-free) | amd64 |
bullseye | 34.0+dfsg-2 (non-free) | amd64 |
trixie | 51.0+dfsg-2 | amd64,arm64,mips64el |
sid | 51.0+dfsg-2 | amd64,arm64,mips64el |
stretch | 1.25.0+dfsg-1 (non-free) | amd64 |
jessie | 1.12.3+dfsg-1 (non-free) | amd64 |
Debtags of package ugene: |
uitoolkit | qt |
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License: DFSG free
|
Unipro UGENE is a cross-platform visual environment for DNA and protein
sequence analysis. UGENE integrates the most important bioinformatics
computational algorithms and provides an easy-to-use GUI for performing
complex analysis of the genomic data. One of the main features of UGENE
is a designer for custom bioinformatics workflows.
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umap-learn
Uniform Manifold Approximation and Projection
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Versions of package umap-learn |
Release | Version | Architectures |
bullseye | 0.4.5+dfsg-2 | all |
bookworm | 0.5.3+dfsg-2 | all |
sid | 0.5.4+dfsg-1 | all |
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License: DFSG free
|
Uniform Manifold Approximation and Projection (UMAP) is a dimension
reduction technique that can be used for visualisation similarly to t-
SNE, but also for general non-linear dimension reduction. The algorithm
is founded on three assumptions about the data:
1. The data is uniformly distributed on a Riemannian manifold;
2. The Riemannian metric is locally constant (or can be
approximated as such);
3. The manifold is locally connected.
From these assumptions it is possible to model the manifold with a fuzzy
topological structure. The embedding is found by searching for a low
dimensional projection of the data that has the closest possible
equivalent fuzzy topological structure.
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umis
tools for processing UMI RNA-tag data
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Versions of package umis |
Release | Version | Architectures |
sid | 1.0.9-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
bullseye | 1.0.7-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
trixie | 1.0.9-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
bookworm | 1.0.8-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
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License: DFSG free
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Umis provides tools for estimating expression in RNA-Seq data which
performs sequencing of end tags of transcript, and incorporate molecular
tags to correct for amplification bias.
There are four steps in this process.
1. Formatting reads
2. Filtering noisy cellular barcodes
3. Pseudo-mapping to cDNAs
4. Counting molecular identifiers
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uncalled
Utility for Nanopore Current Alignment to Large Expanses of DNA
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Versions of package uncalled |
Release | Version | Architectures |
bullseye | 2.2+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.3+ds-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 2.3+ds-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.2+ds1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
Streaming algorithm for mapping raw nanopore signal to DNA references
Enables real-time enrichment or depletion on Oxford Nanopore Technologies
(ONT) MinION runs via ReadUntil.
Also supports standalone signal mapping of fast5 reads
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unicycler
hybrid assembly pipeline for bacterial genomes
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Versions of package unicycler |
Release | Version | Architectures |
sid | 0.5.1+dfsg-1.1 | amd64 |
stretch-backports | 0.4.7+dfsg-1~bpo9+1 | amd64 |
buster | 0.4.7+dfsg-2 | amd64 |
stretch-backports-sloppy | 0.4.8+dfsg-1~bpo9+1 | amd64 |
bullseye | 0.4.8+dfsg-2 | amd64 |
experimental | 0.5.1+dfsg-2 | amd64 |
trixie | 0.5.1+dfsg-1.1 | amd64 |
bookworm | 0.5.0+dfsg-1 | amd64 |
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License: DFSG free
|
Unicycler is an assembly pipeline for bacterial genomes. It can assemble
Illumina-only read sets where it functions as a SPAdes-optimiser. It can
also assembly long-read-only sets (PacBio or Nanopore) where it runs a
miniasm+Racon pipeline. For the best possible assemblies, give it both
Illumina reads and long reads, and it will conduct a hybrid assembly.
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unikmer
Toolkit for nucleic acid k-mer analysis
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Versions of package unikmer |
Release | Version | Architectures |
sid | 0.20.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.19.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.20.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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unikmer is a golang package and a toolkit for nucleic acid k-mer
analysis, providing functions including set operation k-mers
optional with TaxIDs but without count information.
K-mers are either encoded (k<=32) or hashed (arbitrary k) into uint64,
and serialized in binary file with extension .unik.
TaxIDs can be assigned when counting k-mers from genome
sequences, and LCA (Lowest Common Ancestor) is computed during set
opertions including computing union, intersecton, set difference,
unique and repeated k-mers.
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varna
Visualization Applet for RNA
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Versions of package varna |
Release | Version | Architectures |
stretch | 3-93+ds-1 | all |
bookworm | 3-93+ds-4 | all |
trixie | 3-93+ds-7 | all |
sid | 3-93+ds-7 | all |
buster | 3-93+ds-2 | all |
bullseye | 3-93+ds-3 | all |
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License: DFSG free
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VARNA is Java lightweight Applet dedicated to drawing the secondary structure
of RNA. It is also a Swing component that can be very easily included in an
existing Java code working with RNA secondary structure to provide a fast and
interactive visualization.
Being free of fancy external library dependency and/or network access, the
VARNA Applet can be used as a base for a standalone applet. It looks
reasonably good and scales up or down nicely to adapt to the space available
on a web page, thanks to the anti-aliasing drawing primitives of Swing.
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vcfanno
annotate a VCF with other VCFs/BEDs/tabixed files
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Versions of package vcfanno |
Release | Version | Architectures |
trixie | 0.3.5+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.3.2+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.3.5+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.3.5+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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Vcfanno allows you to quickly annotate your VCF with any number of INFO
fields from any number of VCFs or BED files. It uses a simple conf file
to allow the user to specify the source annotation files and fields and
how they will be added to the info of the query VCF.
- For VCF, values are pulled by name from the INFO field with special
cases of ID and FILTER to pull from those VCF columns.
- For BED, values are pulled from (1-based) column number.
- For BAM, depth (count), "mapq" and "seq" are currently supported.
Vcfanno is written in go and it supports custom user-scripts written in
Lua. It can annotate more than 8000 variants per second with 34
annotations from 9 files on a modest laptop and over 30K variants per
second using 12 processes on a server.
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vcftools
Collection of tools to work with VCF files
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Versions of package vcftools |
Release | Version | Architectures |
sid | 0.1.16-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.1.16-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.1.16-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 0.1.14+dfsg-4+deb9u1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0.1.12+dfsg-1 | amd64,armel,armhf,i386 |
bullseye | 0.1.16-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie-security | 0.1.12+dfsg-1+deb8u1 | amd64,armel,armhf,i386 |
buster | 0.1.16-1 | amd64,arm64,armhf,i386 |
Debtags of package vcftools: |
role | program |
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License: DFSG free
|
VCFtools is a program package designed for working with VCF files, such as
those generated by the 1000 Genomes Project. The aim of VCFtools is to
provide methods for working with VCF files: validating, merging, comparing
and calculate some basic population genetic statistics.
The package is enhanced by the following packages:
multiqc
Please cite:
Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert E. Handsaker, Gerton Lunter, Gabor T. Marth, Stephen T. Sherry, Gilean McVean and Richard Durbin:
The variant call format and VCFtools.
(PubMed,eprint)
Bioinformatics
27(15):2156-8
(2011)
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velvet
Nucleic acid sequence assembler for very short reads
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Versions of package velvet |
Release | Version | Architectures |
jessie | 1.2.10+dfsg1-1 | amd64,armel,armhf,i386 |
stretch | 1.2.10+dfsg1-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.2.10+dfsg1-5 | amd64,arm64,armhf,i386 |
bullseye | 1.2.10+dfsg1-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.2.10+dfsg1-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.2.10+dfsg1-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.2.10+dfsg1-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package velvet: |
biology | nuceleic-acids |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
use | analysing |
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License: DFSG free
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Velvet is a de novo genomic assembler specially designed for short read
sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and
Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near
Cambridge, in the United Kingdom.
Velvet currently takes in short read sequences, removes errors then produces
high quality unique contigs. It then uses paired read information, if
available, to retrieve the repeated areas between contigs.
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velvet-long
Nucleic acid sequence assembler for very short reads, long version
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Versions of package velvet-long |
Release | Version | Architectures |
trixie | 1.2.10+dfsg1-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.2.10+dfsg1-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.2.10+dfsg1-1 | amd64,armel,armhf,i386 |
stretch | 1.2.10+dfsg1-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.2.10+dfsg1-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.2.10+dfsg1-5 | amd64,arm64,armhf,i386 |
bullseye | 1.2.10+dfsg1-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
Velvet is a de novo genomic assembler specially designed for short read
sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and
Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near
Cambridge, in the United Kingdom.
Velvet currently takes in short read sequences, removes errors then produces
high quality unique contigs. It then uses paired read information, if
available, to retrieve the repeated areas between contigs.
This package installs special long-mode versions of Velvet, as recommended
in the Velvet tutorials.
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velvetoptimiser
automatically optimise Velvet do novo assembly parameters
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Versions of package velvetoptimiser |
Release | Version | Architectures |
trixie | 2.2.6-5 | all |
bookworm | 2.2.6-5 | all |
bullseye | 2.2.6-3 | all |
sid | 2.2.6-5 | all |
buster | 2.2.6-2 | all |
jessie | 2.2.5-2 | all |
stretch | 2.2.5-5 | all |
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License: DFSG free
|
VelvetOptimiser is a multi-threaded Perl script for automatically optimising
the three primary parameter options (K, -exp_cov, -cov_cutoff) for the Velvet
de novo sequence assembler.
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veryfasttree
Speeding up the estimation of phylogenetic trees from sequences
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Versions of package veryfasttree |
Release | Version | Architectures |
trixie | 4.0.4+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 4.0.4+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
|
VeryFastTree is a highly efficient implementation inspired by the FastTree-2
tool, designed to expedite the inference of approximately-maximum-likelihood
phylogenetic trees from nucleotide or protein sequence alignments. It is an
optimized implementation designed to accelerate the estimation of phylogenies
for large alignments. By leveraging parallelization and vectorization
strategies, VeryFastTree significantly improves the performance and
scalability of phylogenetic analysis, allowing it to construct phylogenetic
trees in a fraction of the time previously required.
Maintaining the integrity of FastTree-2, VeryFastTree retains the same phases,
methods, and heuristics used for estimating phylogenetic trees. This ensures
that the topological accuracy of the trees produced by VeryFastTree remains
equivalent to that of FastTree-2. Moreover, unlike the parallel version of
FastTree-2, VeryFastTree guarantees deterministic results, eliminating any
potential variations in the output.
To facilitate a seamless transition for users, VeryFastTree adopts the exact
same command line arguments as FastTree-2. This means that by simply
substituting FastTree-2 with VeryFastTree, and using the same set of options,
users can significantly enhance the overall performance of their phylogenetic
analyses.
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vg
tools for working with genome variation graphs
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Versions of package vg |
Release | Version | Architectures |
sid | 1.59.0+ds-0.1 | amd64,arm64 |
bullseye | 1.30.0+ds-1 | amd64,mips64el |
upstream | 1.62.0 |
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License: DFSG free
|
variation graph data structures, interchange formats, alignment, genotyping,
and variant calling methods
Variation graphs provide a succinct encoding of the sequences of many genomes.
A variation graph (in particular as implemented in vg) is composed of:
- nodes, which are labeled by sequences and ids
- edges, which connect two nodes via either of their respective ends
- paths, describe genomes, sequence alignments, and annotations (such as gene
models and transcripts) as walks through nodes connected by edges
This model is similar to a number of sequence graphs that have been used in
assembly and multiple sequence alignment. Paths provide coordinate systems
relative to genomes encoded in the graph, allowing stable mappings to be
produced even if the structure of the graph is changed.
Please cite:
Erik Garrison, Jouni Sirén, Adam M Novak, Glenn Hickey, Jordan M Eizenga, Eric T Dawson, William Jones, Shilpa Garg, Charles Markello, Michael F Lin, Benedict Paten and Richard Durbin:
Variation graph toolkit improves read mapping by representing genetic variation in the reference.
(PubMed)
Nature Biotechnology
36(9):875–879
(2018)
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viewmol
graphical front end for computational chemistry programs
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Versions of package viewmol |
Release | Version | Architectures |
stretch | 2.4.1-24 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.4.1-22 | amd64,armel,armhf,i386 |
buster | 2.4.1-25 | amd64,arm64,armhf,i386 |
Debtags of package viewmol: |
field | chemistry |
interface | 3d, x11 |
role | program |
uitoolkit | motif |
use | learning, viewing |
x11 | application |
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License: DFSG free
|
Viewmol is able to graphically aid in the generation of molecular
structures for computations and to visualize their results.
At present Viewmol includes input filters for Discover, DMol3, Gamess,
Gaussian 9x/03, Gulp, Mopac, PQS, Turbomole, and Vamp outputs as well as
for PDB files. Structures can be saved as Accelrys' car-files, MDL files,
and Turbomole coordinate files. Viewmol can generate input files for
Gaussian 9x/03. Viewmol's file format has been added to OpenBabel so that
OpenBabel can serve as an input as well as an output filter for
coordinates.
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virulencefinder
identify virulence genes in total or partial sequenced isolates of bacteria
|
Versions of package virulencefinder |
Release | Version | Architectures |
bookworm | 2.0.4-3 | all |
trixie | 2.0.5-2 | all |
bullseye | 2.0.3+git20190809.dde157a-3 | all |
sid | 2.0.5-2 | all |
upstream | 3.1.0 |
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License: DFSG free
|
The VirulenceFinder service contains one Python script
virulencefinder.py which is the script of the latest version of the
VirulenceFinder service. VirulenceFinder identifies viruelnce genes in
total or partial sequenced isolates of bacteria - at the moment only E.
coli, Enterococcus, S. aureus and Listeria are available.
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vmatch
large scale sequence analysis software
|
Versions of package vmatch |
Release | Version | Architectures |
sid | 2.3.1+dfsg-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.3.1+dfsg-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.3.1+dfsg-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 2.3.1+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
Vmatch is a versatile software tool for efficiently solving large scale
sequence matching tasks. It subsumes the software tool REPuter, but is
much more general, with a very flexible user interface, and improved space
and time requirements.
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vsearch
tool for processing metagenomic sequences
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Versions of package vsearch |
Release | Version | Architectures |
bullseye | 2.15.2-3 | amd64,arm64,ppc64el |
stretch | 2.3.4-1 | amd64 |
bookworm | 2.22.1-1 | amd64,arm64,ppc64el |
trixie | 2.29.1-1 | amd64,arm64,mips64el,ppc64el,riscv64 |
sid | 2.29.1-1 | amd64,arm64,mips64el,ppc64el,riscv64 |
buster | 2.10.4-1 | amd64 |
upstream | 2.29.2 |
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License: DFSG free
|
Versatile 64-bit multithreaded tool for processing metagenomic sequences,
including searching, clustering, chimera detection, dereplication, sorting,
masking and shuffling
The aim of this project is to create an alternative to the USEARCH tool
developed by Robert C. Edgar (2010). The new tool should:
- have a 64-bit design that handles very large databases and much more
than 4GB of memory
- be as accurate or more accurate than usearch
- be as fast or faster than usearch
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vt
toolset for short variant discovery in genetic sequence data
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Versions of package vt |
Release | Version | Architectures |
bullseye | 0.57721+ds-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.57721+ds-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.57721+ds-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.57721+ds-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
vt is a variant tool set that discovers short variants from Next Generation
Sequencing data.
Vt-normalize is a tool to normalize representation of genetic variants in
the VCF. Variant normalization is formally defined as the consistent
representation of genetic variants in an unambiguous and concise way. In
vt a simple general algorithm to enforce this is implemented.
The package is enhanced by the following packages:
vt-examples
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wham-align
Wisconsin's High-Throughput Alignment Method
|
Versions of package wham-align |
Release | Version | Architectures |
sid | 0.1.5-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.1.5-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.1.5-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.1.5-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
This package provides functionality analogous to BWA or
bowtie in aligning reads from next-generation DNA sequencing
machines against a reference genome.
Please cite:
Yinan Li, Allie Terrell and Jignesh M. Patel:
WHAM: A High-throughput Sequence Alignment Method
(eprint)
Proceedings of the ACM SIGMOD International Conference on Management of Data, SIGMOD 2011, Athens, Greece
(2011)
|
|
wigeon
reimplementation of the Pintail 16S DNA anomaly detection utility
|
Versions of package wigeon |
Release | Version | Architectures |
jessie | 20101212+dfsg-1 | all |
bookworm | 20101212+dfsg1-5 | all |
sid | 20101212+dfsg1-6 | all |
stretch | 20101212+dfsg1-1 | all |
trixie | 20101212+dfsg1-6 | all |
bullseye | 20101212+dfsg1-4 | all |
buster | 20101212+dfsg1-2 | all |
|
License: DFSG free
|
WigeoN examines the sequence conservation between a query and a trusted
reference sequence, both in NAST alignment format. Based on the sequence
identity between the query and the reference sequence, there is an
expected amount of variation among the alignment. If the observed
variation is greater than the 95% quantile of the distribution of
variation observed between non-anomalous sequences, then it is flagged
as an anomaly.
WigeoN is a flexible command-line based reimplementation of the Pintail
algorithm Appl Environ Microbiol. 2005 Dec;7112:7724-36.
WigeoN is useful for flagging chimeras and anomalies only in near
full-length 16S rRNA sequences. WigeoN lacks sensitivity with sequences
less than 1000 bp.
To run WigeoN, you need NAST-formatted sequences generated by the
nast-ier utility.
WigeoN is part of the microbiomeutil suite.
Please cite:
Brian J. Haas, Dirk Gevers, Ashlee M. Earl, Mike Feldgarden, Doyle V. Ward, Georgia Giannoukos, Dawn Ciulla, Diana Tabbaa, Sarah K. Highlander, Erica Sodergren, Barbara Methé, Todd Z. DeSantis, The Human Microbiome Consortium, Joseph F. Petrosino, Rob Knight and Bruce W. Birren:
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.
(PubMed,eprint)
Genome Research
21(3):494-504
(2011)
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|
wise
comparison of biopolymers, like DNA and protein sequences
|
Versions of package wise |
Release | Version | Architectures |
sid | 2.4.1-25 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 2.4.1-23 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.4.1-23 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.4.1-21 | amd64,arm64,armhf,i386 |
jessie | 2.4.1-17 | amd64,armel,armhf,i386 |
trixie | 2.4.1-25 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 2.4.1-19 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package wise: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | comparing |
|
License: DFSG free
|
Wise2 is a package focused on comparisons of biopolymers, commonly DNA
and protein sequences. There are many other packages which do
this, probably the best known being BLAST package (from NCBI) and the
Fasta package (from Bill Pearson). There are other packages, such as
the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused
on hidden Markov models (HMMs) of biopolymers.
Wise2's particular forte is the comparison of DNA sequence at the level
of its protein translation. This comparison allows the simultaneous
prediction of say gene structure with homology based alignment.
Wise2 also contains other algorithms, such as the venerable Smith-Waterman
algorithm, or more modern ones such as Stephen Altschul's generalised
gap penalties, or even experimental ones developed in house, such as
dba. The development of these algorithms is due to the ease of developing
such algorithms in the environment used by Wise2.
Wise2 has also been written with an eye for reuse and maintainability.
Although it is a pure C package you can access its functionality
directly in Perl. Parts of the package (or the entire package) can
be used by other C or C++ programs without namespace clashes as all
externally linked variables have the unique identifier Wise2 prepended.
|
|
xpore
Nanopore analysis of differential RNA modifications
|
Versions of package xpore |
Release | Version | Architectures |
bookworm | 2.1-1 | all |
sid | 2.1-2 | all |
trixie | 2.1-2 | all |
|
License: DFSG free
|
RNA is transcribed from DNA, possibly spliced and exported to the
cytoplasm - fine - but its bases can also be modified, edited, and
not all such modifications are visible by Sanger sequencing methods
and its derivatives.
The Nanopore measures potentials, and if the bases have a different
shape then this is measured - not necessarily in an interpretable manner,
something must be left for mass spectrometry, but one may be pointed
to a difference. And maybe one can even statistically associate such
differences with a molecular or clinical phenotype.
|
|
yaha
find split-read mappings on single-end queries
|
Versions of package yaha |
Release | Version | Architectures |
bookworm | 0.1.83-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.1.83-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.1.83-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 0.1.83-1 | amd64,arm64,armhf,i386 |
bullseye | 0.1.83-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
yaha is an open source, flexible, sensitive and accurate DNA aligner
designed for single-end reads. It supports three major modes of
operation:
- The default “Optimal Query Coverage” (-OQC) mode reports the
best set of alignments that cover the length of each query.
- Using “Filter By Similarity” (-FBS), along with the best set of
alignments, yaha will also output alignments that are highly similar
to an alignment in the best set.
- Finally, yaha can output all the alignments found for each query.
The -OQC and -FBS modes are specifically tuned to form split read
mappings that can be used to accurately identify structural variation
events (deletions, duplications, insertions or inversions) between the
subject query and the reference genome.
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yanagiba
filter low quality Oxford Nanopore reads basecalled with Albacore
|
Versions of package yanagiba |
Release | Version | Architectures |
bullseye | 1.0.0-2 | all |
bookworm | 1.0.0-5 | all |
trixie | 1.0.0-5 | all |
sid | 1.0.0-5 | all |
|
License: DFSG free
|
Yanagiba is used to filter short or low quality Oxford Nanopore reads
which have been basecalled with Albacore. It takes fastq.gz and an
Albacore summary file as input. If no Albacore summary file is provided
attempt to calculate mean qscore from directly from fastq file using
NanoMath. Note: Calculated quality scores appear to be lower for reads
called with Metrichor, you may need to lower your minqual setting in
this case.
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yanosim
read simulator nanopore DRS datasets
|
Versions of package yanosim |
Release | Version | Architectures |
sid | 0.1-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
trixie | 0.1-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
bookworm | 0.1-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
bullseye | 0.1-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
|
License: DFSG free
|
Yanosim has three options:
-
yanosim model:
Creates an model of mismatches, insertions and deletions
based on an alignment of nanopore DRS reads to a
reference. Reads should be aligned to a transcriptome
i.e. without spliced alignment, using minimap2. They
should have the cs tag.
2. yanosim quantify:
Quantify the number of reads mapping to each
transcript in a reference, so that the right number
of reads can be simulated.
3. yanosim simulate:
Given a model created using yanosim model, and
per-transcript read counts created using yanosim
simulate, simulate error-prone long-reads from the
given fasta file.
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|
Official Debian packages with lower relevance
adun.app
Molecular Simulator for GNUstep (GUI)
|
Versions of package adun.app |
Release | Version | Architectures |
bullseye | 0.81-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.81-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.81-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 0.81-13 | amd64,arm64,armhf,i386 |
jessie | 0.81-6 | amd64,armel,armhf,i386 |
stretch | 0.81-9 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.81-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package adun.app: |
field | biology, biology:structural |
interface | x11 |
role | program |
scope | application |
suite | gnustep |
uitoolkit | gnustep |
use | analysing, organizing, viewing |
works-with | 3dmodel, db |
x11 | application |
|
License: DFSG free
|
Adun is a biomolecular simulator that also includes data management and
analysis capabilities. It was developed at the Computational Biophysics
and Biochemistry Laboratory, a part of the Research Unit on Biomedical
Informatics of the UPF.
This package contains UL, the Adun GUI frontend.
|
|
catfishq
|
Versions of package catfishq |
Release | Version | Architectures |
trixie | 1.4.0+ds-1 | all |
sid | 1.4.0+ds-1 | all |
bookworm | 1.4.0+ds-1 | all |
|
License: DFSG free
|
FASTQ is the most common format to store the reads from high-throughput
biological sequencing. This tool takes paths to an arbritary number
of zipped and unzipped FASTQ files and/or folders containing zipped or
unzipped FASTQ files, concatenates them and prints them to standard out
(default) or an unzipped output file.
Supported file extensions are: '.fastq', '.fastq.gz', '.fasta',
'.fasta.gz', '.fa', '.fa.gz', '.fq', '.fq.gz'
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|
conda-package-handling
create and extract conda packages of various formats
|
Versions of package conda-package-handling |
Release | Version | Architectures |
bookworm | 2.0.1-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.3.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.3.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.7.2-2+deb11u1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 2.4.0 |
|
License: DFSG free
|
Cph is an abstraction of conda package handling and a tool for
extracting, creating, and converting between formats.
At the time of writing, the standard conda package format is a .tar.bz2
file. That will need to be maintained for quite a long time, thanks to
the long tail of people using old conda versions. There is a new conda
format, described at https://docs.google.com/document/d/1HGKsbg_j69rKXP-
ihhpCb1kNQSE8Iy3yOsUU2x68x8uw/edit?usp=sharing. This new format is
designed to have much faster metadata access and utilize more modern
compression algorithms, while also facilitating package signing without
adding sidecar files.
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|
dascrubber
alignment-based scrubbing pipeline for DNA sequencing reads
|
Versions of package dascrubber |
Release | Version | Architectures |
bullseye | 1.1-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.1-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.1-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 0~20160601-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.1-1 | amd64,arm64,armhf,i386 |
bookworm | 1.1-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
The Dazzler Scrubbing Suite produces a set of edited reads that are guaranteed
to
- be continuous stretches of the underlying genome (i.e. no unremoved
adapters and not chimers)
- have no very low quality stretches (i.e. the error rate never exceeds some
reasonable maximum, 20% or so in the case of Pacbio data).
Its secondary goal is to do so with the minimum removal of data and splitting
of reads.
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|
dnapi
adapter prediction for small RNA sequencing - utils
|
Versions of package dnapi |
Release | Version | Architectures |
sid | 1.1-3 | all |
bullseye | 1.1-3 | all |
bookworm | 1.1-3 | all |
trixie | 1.1-3 | all |
|
License: DFSG free
|
This package provides de novo adapter prediction (iterative) algorithm
for small RNA sequencing data.
DNApi can predict most 3' adapters correctly with the default
parameters. You can tweak the parameters and can run different
prediction modes.
|
|
emboss-explorer
|
Versions of package emboss-explorer |
Release | Version | Architectures |
jessie | 2.2.0-8 | all |
stretch | 2.2.0-8 | all |
buster | 2.2.0-10 | all |
bullseye | 2.2.0-11 | all |
bookworm | 2.2.0-11 | all |
trixie | 2.2.0-12 | all |
sid | 2.2.0-12 | all |
Debtags of package emboss-explorer: |
biology | emboss |
field | biology, biology:bioinformatics |
interface | web |
role | plugin |
web | application, cgi |
|
License: DFSG free
|
EMBOSS explorer is a web-based graphical user interface
to the EMBOSS suite of bioinformatics tools. It is written
in Perl.
If you use the Apache HTTP server, you will at most have to restart it before
using EMBOSS explorer. For other web servers, you will have to do the
configuration by yourself.
|
|
getdata
management of external databases
|
Versions of package getdata |
Release | Version | Architectures |
jessie | 0.2-1 | all |
sid | 0.2-4 | all |
trixie | 0.2-4 | all |
bookworm | 0.2-4 | all |
bullseye | 0.2-4 | all |
buster | 0.2-3 | all |
stretch | 0.2-1 | all |
|
License: DFSG free
|
Many scientific communities share the problem of regularly updating
external databases. With every update, also various tasks need to
be performed for the update of indices that need to be recreated.
This work depends on the tools that are available locally and is
not always completely simple.
This package provides the getData Perl script, which in some not
so complicated manner performs the invocation to wget to download
data and then knows how to perform the indexing. There is only
a hash table to be filled with the commands to be executed.
Maintainers of scientific packages that are strongly coupled to
public datasets are invited to add a runtime dependency to this
package and add instructions for getData to follow.
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|
hts-nim-tools
tools biological sequences: bam-filter, count-reads, vcf-check
|
Versions of package hts-nim-tools |
Release | Version | Architectures |
sid | 0.2.1-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
bullseye | 0.2.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
bookworm | 0.2.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
|
License: DFSG free
|
This package provides several tools that (at least at the time of their
creation) provide functionalities beyond the routine provided by samtools
and other reverse dependencies of the htslib.
These new tools are
• bam-filter : filter BAM/CRAM/SAM files with a simple expression language
• count-reads: count BAM/CRAM reads in regions given in a BED file
• vcf-check : check regions of a VCF against a background for missing chunks
and yes, as the name suggests, these tools are all implemented in nim,
using the nim-hts (upstream: hts-nim) wrapper for the htslib.
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|
idseq-bench
Benchmark generator for the IDseq Portal
|
Versions of package idseq-bench |
Release | Version | Architectures |
sid | 0.0~git20210602.27fb6dc-1 | all |
bullseye | 0.0~git20200902.8241a9a-1 | all |
bookworm | 0.0~git20210602.27fb6dc-1 | all |
|
License: DFSG free
|
IDseq (Infectious Disease Sequencing Platform) is an unbiased global
software platform that helps scientists identify pathogens in
metagenomic sequencing data.
- Discover - Identify the pathogen landscape
- Detect - Monitor and review potential outbreaks
- Decipher - Find potential infecting organisms in large datasets
This package provides the benchmark generator for the IDseq Portal.
|
|
illustrate
cartoonish representations of large biological molecules
|
Versions of package illustrate |
Release | Version | Architectures |
bookworm | 0.0+git20200923.217db48-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.0+git20200923.217db48-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.0+git20200923.217db48-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 0.0+git20240817.e469df4 |
|
License: DFSG free
|
This package provides a binary to transform PDF-formatted proteins into
simplified but instructive graphics. The software has been used for
the Protein-of-the-month's biomolecular illustrations for the past 20
years.
|
|
libhdf5-dev
HDF5 - development files - serial version
|
Versions of package libhdf5-dev |
Release | Version | Architectures |
trixie | 1.10.10+repack-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.10.8+repack1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster-security | 1.10.4+repack-10+deb10u1 | amd64,arm64,armhf,i386 |
bullseye | 1.10.6+repack-4+deb11u1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.10.4+repack-10 | amd64,arm64,armhf,i386 |
jessie-security | 1.8.13+docs-15+deb8u1 | amd64,armel,armhf,i386 |
jessie | 1.8.13+docs-15+deb8u1 | amd64,armel,armhf,i386 |
stretch | 1.10.0-patch1+docs-3+deb9u1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.14.5+repack-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package libhdf5-dev: |
devel | library |
role | devel-lib |
|
License: DFSG free
|
Hierarchical Data Format 5 (HDF5) is a file format and library for
storing scientific data. HDF5 was designed and implemented to address
the deficiencies of HDF4.x. It has a more powerful and flexible data
model, supports files larger than 2 GB, and supports parallel I/O.
This package contains development files for serial platforms.
|
|
libhnswlib-dev
fast approximate nearest neighbor search
|
Versions of package libhnswlib-dev |
Release | Version | Architectures |
bullseye | 0.4.0-3+deb11u1 | all |
trixie | 0.8.0-1 | all |
sid | 0.8.0-1 | all |
bookworm | 0.6.2-2+deb12u1 | all |
|
License: DFSG free
|
Header-only C++ HNSW implementation with Python bindings.
A common task in data analysis but also in scientific computations
is to find data that is very close (multi-dimensional space) or
similar (same thing) to a given data point. Also as heuristics for
physics engines, it is the objects closest to you that you are
most likely to collide with. This library knows how to do this
fast.
|
|
maude
high-performance logical framework
|
Versions of package maude |
Release | Version | Architectures |
trixie | 3.4-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
stretch | 2.7-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.7-2 | amd64,arm64,armhf,i386 |
jessie | 2.6-6 | amd64,armel,armhf,i386 |
bullseye | 3.1-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.2-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 3.4-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
upstream | 3.5 |
Debtags of package maude: |
uitoolkit | ncurses |
|
License: DFSG free
|
Maude is a high-performance reflective language and system supporting
both equational and rewriting logic specification and programming for
a wide range of applications. Maude has been influenced in important
ways by the OBJ3 language, which can be regarded as an equational
logic sublanguage. Besides supporting equational specification and
programming, Maude also supports rewriting logic computation.
Rewriting logic is a logic of concurrent change that can naturally
deal with state and with concurrent computations. It has good
properties as a general semantic framework for giving executable
semantics to a wide range of languages and models of concurrency. In
particular, it supports very well concurrent object-oriented
computation. The same reasons making rewriting logic a good semantic
framework make it also a good logical framework, that is, a metalogic
in which many other logics can be naturally represented and executed.
Maude supports in a systematic and efficient way logical
reflection. This makes Maude remarkably extensible and powerful,
supports an extensible algebra of module composition operations, and
allows many advanced metaprogramming and metalanguage
applications. Indeed, some of the most interesting applications of
Maude are metalanguage applications, in which Maude is used to create
executable environments for different logics, theorem provers,
languages, and models of computation.
Maude is of interest to the biomedical community for modeling and
analysis of biological systems.
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|
metastudent-data
predictor of Gene Ontology terms from protein sequence - data files
|
Versions of package metastudent-data |
Release | Version | Architectures |
stretch | 2.0.1-2 | all |
bookworm | 2.0.1-8 | all |
jessie | 1.0.1-2 | all |
sid | 2.0.1-8 | all |
trixie | 2.0.1-8 | all |
bullseye | 2.0.1-7 | all |
buster | 2.0.1-4 | all |
|
License: DFSG free
|
Often, only the sequence of a protein is known, but
not its functions. Metastudent will try to predict
missing functional annotations through homology searches (BLAST).
All predicted functions correspond to Gene Ontology (GO)
terms from the Molecular Function Ontology (MFO) and the Biological Process
Ontology (BPO) and are associated with a reliability score.
This package contains data files for metastudent.
Please cite:
Tobias Hamp, Rebecca Kassner, Stefan Seemayer, Esmeralda Vicedo, Christian Schaefer, Dominik Achten, Florian Auer, Ariane Boehm, Tatjana Braun, Maximilian Hecht, Mark Heron, Peter Hönigschmid, Thomas A. Hopf, Stefanie Kaufmann, Michael Kiening, Denis Krompass, Cedric Landerer, Yannick Mahlich, Manfred Roos and Burkhard Rost:
Homology-based inference sets the bar high for protein function prediction.
(PubMed)
BMC Bioinformatics
14(Suppl 3):S7
(2013)
|
|
metastudent-data-2
predictor of Gene Ontology terms from protein sequence - data #2
|
Versions of package metastudent-data-2 |
Release | Version | Architectures |
sid | 1.0.0-6 | all |
bookworm | 1.0.0-6 | all |
buster | 1.0.0-4 | all |
jessie | 1.0.0-1 | all |
trixie | 1.0.0-6 | all |
stretch | 1.0.0-2 | all |
bullseye | 1.0.0-5 | all |
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License: DFSG free
|
Often, only the sequence of a protein is known, but
not its functions. Metastudent will try to predict
missing functional annotations through homology searches (BLAST).
All predicted functions correspond to Gene Ontology (GO)
terms from the Molecular Function Ontology (MFO) and the Biological Process
Ontology (BPO) and are associated with a reliability score.
This package contains additional data files for metastudent.
Please cite:
Tobias Hamp, Rebecca Kassner, Stefan Seemayer, Esmeralda Vicedo, Christian Schaefer, Dominik Achten, Florian Auer, Ariane Boehm, Tatjana Braun, Maximilian Hecht, Mark Heron, Peter Hönigschmid, Thomas A. Hopf, Stefanie Kaufmann, Michael Kiening, Denis Krompass, Cedric Landerer, Yannick Mahlich, Manfred Roos and Burkhard Rost:
Homology-based inference sets the bar high for protein function prediction.
(PubMed)
BMC Bioinformatics
14(Suppl 3):S7
(2013)
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mrs
Information Retrieval System for Biomedical databanks
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Versions of package mrs |
Release | Version | Architectures |
buster | 6.0.5+dfsg-7 | amd64,arm64,armhf,i386 |
stretch | 6.0.5+dfsg-2 | amd64 |
jessie | 6.0.5+dfsg-1 | amd64 |
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License: DFSG free
|
MRS is a complete system to retrieve, index and query biological and
medical databanks. It comes with all the code required to fetch data
using FTP or rsync, then creates a local databank with indices using
a databank specific parser written in Perl. It can then serve this
data using a built-in web application and webservices.
Searching can be done on words and Boolean queries. As a bonus you
can search protein sequences using a custom Blast algorithm.
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python3-alignlib
edit and Hamming distances for biological sequences
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Versions of package python3-alignlib |
Release | Version | Architectures |
bookworm | 0.1.1+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.1.1+dfsg-1.1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.1.1+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.1.1+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
|
A small Python module providing edit distance and Hamming distance
computation. It is a dependency for the IgDiscover package and
likely future others.
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python3-anndata
annotated gene by sample numpy matrix
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Versions of package python3-anndata |
Release | Version | Architectures |
bullseye | 0.7.5+ds-3 | all |
sid | 0.10.6-1 | all |
bookworm | 0.8.0-4 | all |
upstream | 0.11.1 |
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License: DFSG free
|
AnnData provides a scalable way of keeping track of data together
with learned annotations. It is used within Scanpy, for which it was
initially developed. Both packages have been introduced in Genome
Biology (2018).
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python3-cgecore
Python3 module for the Center for Genomic Epidemiology
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Versions of package python3-cgecore |
Release | Version | Architectures |
bullseye | 1.5.6+ds-1 | all |
sid | 1.5.6+ds-2 | all |
trixie | 1.5.6+ds-2 | all |
bookworm | 1.5.6+ds-1 | all |
upstream | 2.0.0 |
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License: DFSG free
|
This Python3 module contains classes and functions needed to run the
service wrappers and pipeline scripts developed by the Center for
Genomic Epidemiology.
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python3-cyvcf2
VCF parser based on htslib (Python 3)
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Versions of package python3-cyvcf2 |
Release | Version | Architectures |
trixie | 0.31.1-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.30.4-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.30.18-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.31.1-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 0.10.4-1 | amd64,arm64,armhf,i386 |
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License: DFSG free
|
This modules allows fast parsing of VCF and BCF including region-queries
with Python. This is essential for efficient analyses of nucleotide
variation with Python on high-throughput sequencing data.
cyvcf2 is a cython wrapper around htslib. Attributes like
variant.gt_ref_depths return a numpy array directly so they are
immediately ready for downstream use.
This package installs the library for Python 3.
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python3-deeptools
platform for exploring biological deep-sequencing data
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Versions of package python3-deeptools |
Release | Version | Architectures |
bullseye | 3.5.0-1 | all |
bookworm | 3.5.1-3 | all |
trixie | 3.5.5+dfsg-1 | all |
sid | 3.5.5+dfsg-1 | all |
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License: DFSG free
|
Aiming for compatibility with the Galaxy worklfow environment, but
also independently contributing to a series of workflows in
genomics, this package provides a series of tools to address
common tasks for the processing of high-throughput DNA/RNA sequencing.
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python3-deeptoolsintervals
handlig GTF-like sequence-associated interal-annotation
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Versions of package python3-deeptoolsintervals |
Release | Version | Architectures |
bookworm | 0.1.9-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.1.9-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.1.9-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.1.9-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
|
Regions in biological sequences are described (annotated) as genes,
transcription factor binding sites, low complexity, ... whatever
biological research brings.
This package supports the efficienct operation with this information.
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python3-htseq
Python3 high-throughput genome sequencing read analysis utilities
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Versions of package python3-htseq |
Release | Version | Architectures |
buster | 0.11.2-1 | amd64,arm64 |
sid | 2.0.9+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
bookworm | 1.99.2-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
bullseye | 0.13.5-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
trixie | 2.0.9+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
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License: DFSG free
|
HTSeq can be used to performing a number of common analysis tasks
when working with high-throughput genome sequencing reads:
- Getting statistical summaries about the base-call quality scores to
study the data quality.
- Calculating a coverage vector and exporting it for visualization in
a genome browser.
- Reading in annotation data from a GFF file.
- Assigning aligned reads from an RNA-Seq experiments to exons and
genes.
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python3-intake
lightweight package for finding and investigating data
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Versions of package python3-intake |
Release | Version | Architectures |
sid | 0.6.6-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.6.6-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 2.0.7 |
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License: DFSG free
|
Intake is a lightweight set of tools for loading and sharing data in
data science projects. Intake helps you:
1. Load data from a variety of formats into containers you already know,
like Pandas dataframes, Python lists, NumPy arrays and more.
2. Convert boilerplate data loading code into reusable intake plugins.
3. Describe data sets in catalog files for easy reuse and sharing
between projects and with others.
4. Share catalog information (and data sets) over the network with the
Intake server.
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python3-loompy
access loom formatted files for bioinformatics
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Versions of package python3-loompy |
Release | Version | Architectures |
sid | 3.0.7+dfsg-3 | amd64,arm64,mips64el,ppc64el,s390x |
bookworm | 3.0.7+dfsg-2 | amd64,arm64,mips64el,ppc64el,s390x |
upstream | 3.0.8 |
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License: DFSG free
|
Loom is an efficient file format for very large omics datasets,
consisting of a main matrix, optional additional layers, a variable
number of row and column annotations. Loom also supports sparse
graphs. Loom files are used to store single-cell gene expression data:
the main matrix contains the actual expression values (one column per
cell, one row per gene); row and column annotations contain metadata
for genes and cells, such as Name, Chromosome, Position (for genes),
and Strain, Sex, Age (for cells).
Loom files (.loom) are created in the HDF5 file format, which supports
an internal collection of numerical multidimensional datasets. HDF5
is supported by many computer languages, including Java, MATLAB,
Mathematica, Python, R, and Julia. .loom files are accessible from any
language that supports HDF5.
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python3-nanoget
extract information from Oxford Nanopore sequencing data and alignments
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Versions of package python3-nanoget |
Release | Version | Architectures |
bookworm | 1.16.1-2 | all |
sid | 1.19.3-1 | all |
trixie | 1.19.3-1 | all |
bullseye | 1.12.2-4 | all |
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License: DFSG free
|
The Python3 module nanoget provides functions to extract useful metrics
from Oxford Nanopore sequencing reads and alignments.
Data can be presented in the following formats, using the following functions:
- sorted bam file process_bam(bamfile, threads)
- standard fastq file process_fastq_plain(fastqfile, 'threads')
- fastq file with metadata from MinKNOW or Albacore
process_fastq_rich(fastqfile)
- sequencing_summary file generated by Albacore
process_summary(sequencing_summary.txt, 'readtype')
Fastq files can be compressed using gzip, bzip2 or bgzip. The data is
returned as a pandas DataFrame with standardized headernames for
convenient extraction. The functions perform logging while being called
and extracting data.
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python3-nanomath
simple math function for other Oxford Nanopore processing scripts
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Versions of package python3-nanomath |
Release | Version | Architectures |
sid | 1.2.1+ds-1 | all |
bookworm | 1.2.1+ds-1 | all |
trixie | 1.2.1+ds-1 | all |
bullseye | 1.2.0+ds-1 | all |
upstream | 1.4.0 |
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License: DFSG free
|
This Python3 module provides a few simple math and statistics functions for
other scripts processing Oxford Nanopore sequencing data.
- Calculate read N50 from a set of lengths get_N50(readlenghts)
- Remove extreme length outliers from a dataset
remove_length_outliers(dataframe, columname)
- Calculate the average Phred quality of a read ave_qual(qualscores)
- Write out the statistics report after calling readstats function
write_stats(dataframe, outputname)
- Compute a number of statistics, return a dictionary
calc_read_stats(dataframe)
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python3-ncls
datastructure for interval overlap queries
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Versions of package python3-ncls |
Release | Version | Architectures |
bullseye | 0.0.57+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.0.63-hotfix+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.0.63-hotfix+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.0.63-hotfix+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
The Nested Containment List is a datastructure for interval overlap
queries, like the interval tree. It is usually an order of magnitude
faster than the interval tree both for building and query lookups.
The implementation here is a revived version of the one used in the
now defunct PyGr library, which died of bitrot. It was now made less
memory-consuming and wrapper functions allow batch-querying
the NCLS for further speed gains.
This package was implemented to be the cornerstone of the PyRanges project,
but was made available to the Python community as a stand-alone library.
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python3-py2bit
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Versions of package python3-py2bit |
Release | Version | Architectures |
bullseye | 0.3.0-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
trixie | 0.3.2-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
sid | 0.3.2-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
bookworm | 0.3.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
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License: DFSG free
|
From https://genome.ucsc.edu/FAQ/FAQformat.html#format7:
A .2bit file stores multiple DNA sequences (up to 4 Gb total) in a
compact randomly-accessible format. The file contains masking information
as well as the DNA itself.
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python3-pybel
Biological Expression Language
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Versions of package python3-pybel |
Release | Version | Architectures |
sid | 0.15.5-1 | all |
bullseye | 0.14.10-1 | all |
bookworm | 0.14.10-1 | all |
buster | 0.12.1-1 | all |
trixie | 0.15.5-1 | all |
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License: DFSG free
|
PyBEL is a pure Python package for parsing and handling biological
networks encoded in the Biological Expression Language (BEL) version
2. It also facilitates data interchange between common formats and
databases such as NetworkX, JSON, CSV, SIF, Cytoscape, CX, NDEx, SQL,
and Neo4J.
This package installs the library for Python 3.
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python3-pychopper
identify, orient and trim full-length Nanopore cDNA reads
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Versions of package python3-pychopper |
Release | Version | Architectures |
bookworm | 2.7.2-1 | all |
sid | 2.7.10-1 | all |
bullseye | 2.5.0-1 | all |
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License: DFSG free
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Pychopper v2 is a Python module to identify, orient and trim full-length
Nanopore cDNA reads. It is also able to rescue fused reads and provides
the script 'pychopper.py'. The general approach of Pychopper v2
is the following:
- Pychopper first identifies alignment hits of the primers across the
length of the sequence. The default method for doing this is using
nhmmscan with the pre-trained strand specific profile HMMs, included
with the package. Alternatively, one can use the edlib backend,
which uses a combination of global and local alignment to identify
the primers within the read.
- After identifying the primer hits by either of the backends, the
reads are divided into segments defined by two consecutive primer
hits. The score of a segment is its length if the configuration of
the flanking primer hits is valid (such as SPP,-VNP for forward reads)
or zero otherwise.
- The segments are assigned to rescued reads using a dynamic programming
algorithm maximizing the sum of used segment scores (hence the amount
of rescued bases). A crucial observation about the algorithm is that
if a segment is included as a rescued read, then the next segment
must be excluded as one of the primer hits defining it was "used
up" by the previous segment. This put constraints on the dynamic
programming graph. The arrows in read define the optimal path for
rescuing two fused reads with the a total score of l1 + l3.
A crucial parameter of Pychopper v2 is -q, which determines the
stringency of primer alignment (E-value in the case of the pHMM
backend). This can be explicitly specified by the user, however by
default it is optimized on a random sample of input reads to produce
the maximum number of classified reads.
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python3-pyfaidx
efficient random access to fasta subsequences for Python 3
|
Versions of package python3-pyfaidx |
Release | Version | Architectures |
stretch | 0.4.8.1-1 | all |
bookworm | 0.7.1-2 | all |
sid | 0.8.1.3-1 | all |
bullseye | 0.5.9.2-1 | all |
trixie | 0.8.1.3-1 | all |
buster | 0.5.5.2-1 | all |
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License: DFSG free
|
Samtools provides a function "faidx" (FAsta InDeX), which creates a
small flat index file ".fai" allowing for fast random access to any
subsequence in the indexed FASTA file, while loading a minimal amount of
the file in to memory. This Python module implements pure Python classes
for indexing, retrieval, and in-place modification of FASTA files using
a samtools compatible index. The pyfaidx module is API compatible with
the pygr seqdb module. A command-line script "faidx" is installed
alongside the pyfaidx module, and facilitates complex manipulation of
FASTA files without any programming knowledge.
This package provides the Python 3 modules to access fasta files.
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python3-pyflow
??? missing short description for package python3-pyflow :-(
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Versions of package python3-pyflow |
Release | Version | Architectures |
bullseye | 1.1.20-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.1.20-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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python3-pyranges
2D representation of genomic intervals and their annotations
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Versions of package python3-pyranges |
Release | Version | Architectures |
trixie | 0.0.111+ds-8 | all |
bookworm | 0.0.111+ds-4 | all |
sid | 0.0.111+ds-8 | all |
bullseye | 0.0.85+ds-1 | all |
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License: DFSG free
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A PyRanges object must have the columns Chromosome, Start and
End. These describe the genomic position and function as implicit row
labels. A Strand column is optional and adds strand information to the
intervals. Any other columns are allowed and are considered metadata.
The structure can be filled from .bed, .bam or .gff files, also from
tabular or textual representations.
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python3-pyrle
run length arithmetic in Python
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Versions of package python3-pyrle |
Release | Version | Architectures |
bookworm | 0.0.33-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.0.33-4.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.0.33-4.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.0.31-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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As opposed to S4Vectors, pyrle does not rotate the shortest vector, but
rather extends the shorter Rle with zeroes. This is likely the desired
behavior in almost all cases.
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python3-pysam
interface for the SAM/BAM sequence alignment and mapping format (Python 3)
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Versions of package python3-pysam |
Release | Version | Architectures |
stretch | 0.10.0+ds-2 | amd64,arm64,mips64el,ppc64el |
sid | 0.22.1+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
trixie | 0.22.1+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
bookworm | 0.20.0+ds-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
bullseye | 0.15.4+ds-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
buster | 0.15.2+ds-2 | amd64,arm64 |
stretch-backports | 0.14+ds-2~bpo9+1 | amd64,arm64,mips64el,ppc64el |
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License: DFSG free
|
Pysam is a Python module for reading and manipulating Samfiles. It's a
lightweight wrapper of the samtools C-API. Pysam also includes an interface
for tabix.
This package installs the module for Python 3.
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python3-tinyalign
numerical representation of differences between strings
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Versions of package python3-tinyalign |
Release | Version | Architectures |
sid | 0.2.2-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.2.2-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.2-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.2.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
A small Python module providing edit distance (aka Levenshtein distance,
that is, counting insertions, deletions and substitutions) and Hamming
distance computation.
Its main purpose is to speed up computation of edit distance by allowing
to specify a maximum number of differences maxdiff (banding). If that
parameter is provided, the returned edit distance is anly accurate up
to maxdiff. That is, if the actual edit distance is higher than maxdiff,
a value larger than maxdiff is returned, but not necessarily the actual
edit distance.
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q2-alignment
QIIME 2 plugin for generating and manipulating alignments
|
Versions of package q2-alignment |
Release | Version | Architectures |
sid | 2024.5.0-1 | all |
bullseye | 2020.11.1-2 | all |
bookworm | 2022.11.1-2 | all |
upstream | 2024.10.0 |
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License: DFSG free
|
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
researchers to start an analysis with raw DNA sequence data and finish with
publication-quality figures and statistical results.
Key features:
- Integrated and automatic tracking of data provenance
- Semantic type system
- Plugin system for extending microbiome analysis functionality
- Support for multiple types of user interfaces (e.g. API, command line,
graphical)
QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis
pipeline. QIIME 2 will address many of the limitations of QIIME 1, while
retaining the features that makes QIIME 1 a powerful and widely-used analysis
pipeline.
QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline.
New functionality will regularly become available through QIIME 2 plugins. You
can view a list of plugins that are currently available on the QIIME 2 plugin
availability page. The future plugins page lists plugins that are being
developed.
Please cite:
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso:
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
(eprint)
Nature Biotechnology
37
(2019)
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q2-cutadapt
QIIME 2 plugin to work with adapters in sequence data
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Versions of package q2-cutadapt |
Release | Version | Architectures |
sid | 2024.5.0-1 | amd64,arm64,mips64el,ppc64el,riscv64 |
bookworm | 2022.11.1-2 | amd64,arm64,mips64el,ppc64el |
bullseye | 2020.11.1-1 | amd64,arm64,mips64el,ppc64el |
upstream | 2024.10.0 |
|
License: DFSG free
|
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
researchers to start an analysis with raw DNA sequence data and finish with
publication-quality figures and statistical results.
Key features:
- Integrated and automatic tracking of data provenance
- Semantic type system
- Plugin system for extending microbiome analysis functionality
- Support for multiple types of user interfaces (e.g. API, command line,
graphical)
QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis
pipeline. QIIME 2 will address many of the limitations of QIIME 1, while
retaining the features that makes QIIME 1 a powerful and widely-used analysis
pipeline.
QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline.
New functionality will regularly become available through QIIME 2 plugins. You
can view a list of plugins that are currently available on the QIIME 2 plugin
availability page. The future plugins page lists plugins that are being
developed.
Please cite:
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso:
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
(eprint)
Nature Biotechnology
37
(2019)
|
|
q2-dada2
QIIME 2 plugin to work with adapters in sequence data
|
Versions of package q2-dada2 |
Release | Version | Architectures |
bullseye | 2020.11.1-3 | amd64 |
sid | 2024.5.0-1 | amd64 |
bookworm | 2022.11.2-2 | amd64 |
upstream | 2024.10.0 |
|
License: DFSG free
|
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
researchers to start an analysis with raw DNA sequence data and finish with
publication-quality figures and statistical results.
Key features:
- Integrated and automatic tracking of data provenance
- Semantic type system
- Plugin system for extending microbiome analysis functionality
- Support for multiple types of user interfaces (e.g. API, command line,
graphical)
QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis
pipeline. QIIME 2 will address many of the limitations of QIIME 1, while
retaining the features that makes QIIME 1 a powerful and widely-used analysis
pipeline.
QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline.
New functionality will regularly become available through QIIME 2 plugins. You
can view a list of plugins that are currently available on the QIIME 2 plugin
availability page. The future plugins page lists plugins that are being
developed.
This package wraps the dada2 R package in BioConductor for modeling and
correcting Illumina-sequenced amplicon errors. This was shown to improve the
sensitivity of diversity analyses.
Please cite:
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso:
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
(eprint)
Nature Biotechnology
37
(2019)
|
|
q2-demux
QIIME 2 plugin for demultiplexing of sequence reads
|
Versions of package q2-demux |
Release | Version | Architectures |
bookworm | 2022.11.1+dfsg-2 | all |
sid | 2024.5.0+dfsg-1 | all |
bullseye | 2020.11.1-1 | all |
upstream | 2024.10.0 |
|
License: DFSG free
|
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
researchers to start an analysis with raw DNA sequence data and finish with
publication-quality figures and statistical results.
Key features:
- Integrated and automatic tracking of data provenance
- Semantic type system
- Plugin system for extending microbiome analysis functionality
- Support for multiple types of user interfaces (e.g. API, command line,
graphical)
QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis
pipeline. QIIME 2 will address many of the limitations of QIIME 1, while
retaining the features that makes QIIME 1 a powerful and widely-used analysis
pipeline.
QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline.
New functionality will regularly become available through QIIME 2 plugins. You
can view a list of plugins that are currently available on the QIIME 2 plugin
availability page. The future plugins page lists plugins that are being
developed.
Please cite:
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso:
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
(eprint)
Nature Biotechnology
37
(2019)
|
|
q2-emperor
QIIME2 plugin for display of ordination plots
|
Versions of package q2-emperor |
Release | Version | Architectures |
bookworm | 2022.11.1-2 | all |
sid | 2024.5.0-2 | all |
upstream | 2024.10.0 |
|
License: DFSG free
|
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
researchers to start an analysis with raw DNA sequence data and finish with
publication-quality figures and statistical results.
Key features:
- Integrated and automatic tracking of data provenance
- Semantic type system
- Plugin system for extending microbiome analysis functionality
- Support for multiple types of user interfaces (e.g. API, command line,
graphical)
QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis
pipeline. QIIME 2 will address many of the limitations of QIIME 1, while
retaining the features that makes QIIME 1 a powerful and widely-used analysis
pipeline.
QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline.
New functionality will regularly become available through QIIME 2 plugins. You
can view a list of plugins that are currently available on the QIIME 2 plugin
availability page. The future plugins page lists plugins that are being
developed.
Please cite:
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso:
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
(eprint)
Nature Biotechnology
37
(2019)
|
|
q2-feature-classifier
QIIME 2 plugin supporting taxonomic classification
|
Versions of package q2-feature-classifier |
Release | Version | Architectures |
sid | 2024.2.0-1 | all |
bullseye | 2020.11.1-2 | all |
bookworm | 2022.11.1-2 | all |
upstream | 2024.10.0 |
|
License: DFSG free
|
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
researchers to start an analysis with raw DNA sequence data and finish with
publication-quality figures and statistical results.
Key features:
- Integrated and automatic tracking of data provenance
- Semantic type system
- Plugin system for extending microbiome analysis functionality
- Support for multiple types of user interfaces (e.g. API, command line,
graphical)
QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis
pipeline. QIIME 2 will address many of the limitations of QIIME 1, while
retaining the features that makes QIIME 1 a powerful and widely-used analysis
pipeline.
QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline.
New functionality will regularly become available through QIIME 2 plugins. You
can view a list of plugins that are currently available on the QIIME 2 plugin
availability page. The future plugins page lists plugins that are being
developed.
Please cite:
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso:
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
(eprint)
Nature Biotechnology
37
(2019)
|
|
q2-feature-table
QIIME 2 plugin supporting operations on feature tables
|
Versions of package q2-feature-table |
Release | Version | Architectures |
bookworm | 2022.11.1+dfsg-2 | all |
bullseye | 2020.11.1+dfsg-1 | all |
sid | 2024.5.0+dfsg-1 | all |
upstream | 2024.10.0 |
|
License: DFSG free
|
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
researchers to start an analysis with raw DNA sequence data and finish with
publication-quality figures and statistical results.
Key features:
- Integrated and automatic tracking of data provenance
- Semantic type system
- Plugin system for extending microbiome analysis functionality
- Support for multiple types of user interfaces (e.g. API, command line,
graphical)
QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis
pipeline. QIIME 2 will address many of the limitations of QIIME 1, while
retaining the features that makes QIIME 1 a powerful and widely-used analysis
pipeline.
QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline.
New functionality will regularly become available through QIIME 2 plugins. You
can view a list of plugins that are currently available on the QIIME 2 plugin
availability page. The future plugins page lists plugins that are being
developed.
Please cite:
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso:
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
(eprint)
Nature Biotechnology
37
(2019)
|
|
q2-fragment-insertion
QIIME 2 plugin for fragment insertion
|
Versions of package q2-fragment-insertion |
Release | Version | Architectures |
bookworm | 2022.11.1-3 | amd64,arm64,mips64el,ppc64el |
sid | 2024.5.0-1 | amd64,arm64,mips64el,ppc64el,riscv64 |
upstream | 2024.10.0 |
|
License: DFSG free
|
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
researchers to start an analysis with raw DNA sequence data and finish with
publication-quality figures and statistical results.
Key features:
- Integrated and automatic tracking of data provenance
- Semantic type system
- Plugin system for extending microbiome analysis functionality
- Support for multiple types of user interfaces (e.g. API, command line,
graphical)
QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis
pipeline. QIIME 2 will address many of the limitations of QIIME 1, while
retaining the features that makes QIIME 1 a powerful and widely-used analysis
pipeline.
QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline.
New functionality will regularly become available through QIIME 2 plugins. You
can view a list of plugins that are currently available on the QIIME 2 plugin
availability page. The future plugins page lists plugins that are being
developed.
Please cite:
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso:
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
(eprint)
Nature Biotechnology
37
(2019)
|
|
q2-metadata
QIIME 2 plugin for working with and visualizing Metadata
|
Versions of package q2-metadata |
Release | Version | Architectures |
bookworm | 2022.8.0-1 | amd64,arm64,mips64el,ppc64el |
bullseye | 2020.11.1+dfsg-1 | amd64,arm64,mips64el,ppc64el |
sid | 2024.5.0+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64 |
upstream | 2024.10.0 |
|
License: DFSG free
|
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
researchers to start an analysis with raw DNA sequence data and finish with
publication-quality figures and statistical results.
Key features:
- Integrated and automatic tracking of data provenance
- Semantic type system
- Plugin system for extending microbiome analysis functionality
- Support for multiple types of user interfaces (e.g. API, command line,
graphical)
QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis
pipeline. QIIME 2 will address many of the limitations of QIIME 1, while
retaining the features that makes QIIME 1 a powerful and widely-used analysis
pipeline.
QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline.
New functionality will regularly become available through QIIME 2 plugins. You
can view a list of plugins that are currently available on the QIIME 2 plugin
availability page. The future plugins page lists plugins that are being
developed.
Please cite:
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso:
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
(eprint)
Nature Biotechnology
37
(2019)
|
|
q2-phylogeny
QIIME 2 plugin for phylogeny
|
Versions of package q2-phylogeny |
Release | Version | Architectures |
bookworm | 2022.11.1-3 | amd64 |
sid | 2024.5.0-1 | amd64 |
experimental | 2022.11.1-1 | all |
upstream | 2024.10.0 |
|
License: DFSG free
|
QIIME 2 plugin for phylogenetic reconstruction, and operations on
phylogenetic trees.
|
|
q2-quality-control
QIIME 2 plugin for quality assurance of feature and sequence data
|
Versions of package q2-quality-control |
Release | Version | Architectures |
bookworm | 2022.11.1-2 | all |
sid | 2024.5.0-1 | all |
bullseye | 2020.11.1-3 | all |
upstream | 2024.10.0 |
|
License: DFSG free
|
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
researchers to start an analysis with raw DNA sequence data and finish with
publication-quality figures and statistical results.
Key features:
- Integrated and automatic tracking of data provenance
- Semantic type system
- Plugin system for extending microbiome analysis functionality
- Support for multiple types of user interfaces (e.g. API, command line,
graphical)
QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis
pipeline. QIIME 2 will address many of the limitations of QIIME 1, while
retaining the features that makes QIIME 1 a powerful and widely-used analysis
pipeline.
QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline.
New functionality will regularly become available through QIIME 2 plugins. You
can view a list of plugins that are currently available on the QIIME 2 plugin
availability page. The future plugins page lists plugins that are being
developed.
Please cite:
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso:
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
(eprint)
Nature Biotechnology
37
(2019)
|
|
q2-quality-filter
QIIME2 plugin for PHRED-based filtering and trimming
|
Versions of package q2-quality-filter |
Release | Version | Architectures |
sid | 2024.5.0-1 | all |
bookworm | 2022.11.1-2 | all |
bullseye | 2020.11.1-2 | all |
upstream | 2024.10.0 |
|
License: DFSG free
|
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
researchers to start an analysis with raw DNA sequence data and finish with
publication-quality figures and statistical results.
Key features:
- Integrated and automatic tracking of data provenance
- Semantic type system
- Plugin system for extending microbiome analysis functionality
- Support for multiple types of user interfaces (e.g. API, command line,
graphical)
QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis
pipeline. QIIME 2 will address many of the limitations of QIIME 1, while
retaining the features that makes QIIME 1 a powerful and widely-used analysis
pipeline.
QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline.
New functionality will regularly become available through QIIME 2 plugins. You
can view a list of plugins that are currently available on the QIIME 2 plugin
availability page. The future plugins page lists plugins that are being
developed.
Please cite:
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso:
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
(eprint)
Nature Biotechnology
37
(2019)
|
|
q2-sample-classifier
QIIME 2 plugin for machine learning prediction of sample data
|
Versions of package q2-sample-classifier |
Release | Version | Architectures |
bullseye | 2020.11.1-3 | all |
sid | 2024.5.0-2 | all |
bookworm | 2022.11.1-3 | all |
upstream | 2024.10.0 |
|
License: DFSG free
|
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
researchers to start an analysis with raw DNA sequence data and finish with
publication-quality figures and statistical results.
Key features:
- Integrated and automatic tracking of data provenance
- Semantic type system
- Plugin system for extending microbiome analysis functionality
- Support for multiple types of user interfaces (e.g. API, command line,
graphical)
QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis
pipeline. QIIME 2 will address many of the limitations of QIIME 1, while
retaining the features that makes QIIME 1 a powerful and widely-used analysis
pipeline.
QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline.
New functionality will regularly become available through QIIME 2 plugins. You
can view a list of plugins that are currently available on the QIIME 2 plugin
availability page. The future plugins page lists plugins that are being
developed.
Microbiome studies often aim to predict outcomes or differentiate samples
based on their microbial compositions, tasks that can be efficiently
performed by supervised learning methods. The q2-sample-classifier plugin
makes these methods more accessible, reproducible, and interpretable to
a broad audience of microbiologists, clinicians, and others who wish to
utilize supervised learning methods for predicting sample characteristics
based on microbiome composition or other "omics" data
|
|
q2-taxa
QIIME 2 plugin for working with feature taxonomy annotations
|
Versions of package q2-taxa |
Release | Version | Architectures |
bullseye | 2020.11.1+dfsg-2 | all |
sid | 2024.5.0+dfsg-1 | all |
bookworm | 2022.11.1+dfsg-2 | all |
upstream | 2024.10.0 |
|
License: DFSG free
|
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
researchers to start an analysis with raw DNA sequence data and finish with
publication-quality figures and statistical results.
Key features:
- Integrated and automatic tracking of data provenance
- Semantic type system
- Plugin system for extending microbiome analysis functionality
- Support for multiple types of user interfaces (e.g. API, command line,
graphical)
QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis
pipeline. QIIME 2 will address many of the limitations of QIIME 1, while
retaining the features that makes QIIME 1 a powerful and widely-used analysis
pipeline.
QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline.
New functionality will regularly become available through QIIME 2 plugins. You
can view a list of plugins that are currently available on the QIIME 2 plugin
availability page. The future plugins page lists plugins that are being
developed.
Please cite:
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso:
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
(eprint)
Nature Biotechnology
37
(2019)
|
|
q2-types
QIIME 2 plugin defining types for microbiome analysis
|
Versions of package q2-types |
Release | Version | Architectures |
bookworm | 2022.11.1-2 | all |
sid | 2024.5.0-1 | all |
bullseye | 2020.11.1-1 | all |
upstream | 2024.10.0 |
|
License: DFSG free
|
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
researchers to start an analysis with raw DNA sequence data and finish with
publication-quality figures and statistical results.
Key features:
- Integrated and automatic tracking of data provenance
- Semantic type system
- Plugin system for extending microbiome analysis functionality
- Support for multiple types of user interfaces (e.g. API, command line,
graphical)
QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis
pipeline. QIIME 2 will address many of the limitations of QIIME 1, while
retaining the features that makes QIIME 1 a powerful and widely-used analysis
pipeline.
QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline.
New functionality will regularly become available through QIIME 2 plugins. You
can view a list of plugins that are currently available on the QIIME 2 plugin
availability page. The future plugins page lists plugins that are being
developed.
Please cite:
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso:
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
(eprint)
Nature Biotechnology
37
(2019)
|
|
q2cli
Click-based command line interface for QIIME 2
|
Versions of package q2cli |
Release | Version | Architectures |
bookworm | 2022.11.1-2 | all |
bullseye | 2020.11.1-1 | all |
sid | 2024.5.0-2 | all |
upstream | 2024.10.1 |
|
License: DFSG free
|
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
researchers to start an analysis with raw DNA sequence data and finish with
publication-quality figures and statistical results.
Key features:
- Integrated and automatic tracking of data provenance
- Semantic type system
- Plugin system for extending microbiome analysis functionality
- Support for multiple types of user interfaces (e.g. API, command line,
graphical)
QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis
pipeline. QIIME 2 will address many of the limitations of QIIME 1, while
retaining the features that makes QIIME 1 a powerful and widely-used analysis
pipeline.
QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline.
New functionality will regularly become available through QIIME 2 plugins. You
can view a list of plugins that are currently available on the QIIME 2 plugin
availability page. The future plugins page lists plugins that are being
developed.
Please cite:
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso:
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
(eprint)
Nature Biotechnology
37
(2019)
|
|
q2templates
Design template package for QIIME 2 Plugins
|
Versions of package q2templates |
Release | Version | Architectures |
bookworm | 2022.11.1+ds-2 | all |
trixie | 2024.5.0+ds-1 | all |
sid | 2024.5.0+ds-1 | all |
bullseye | 2020.11.1+dfsg-1 | all |
upstream | 2024.10.0 |
|
License: DFSG free
|
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
researchers to start an analysis with raw DNA sequence data and finish with
publication-quality figures and statistical results.
Key features:
- Integrated and automatic tracking of data provenance
- Semantic type system
- Plugin system for extending microbiome analysis functionality
- Support for multiple types of user interfaces (e.g. API, command line,
graphical)
QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis
pipeline. QIIME 2 will address many of the limitations of QIIME 1, while
retaining the features that makes QIIME 1 a powerful and widely-used analysis
pipeline.
QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline.
New functionality will regularly become available through QIIME 2 plugins. You
can view a list of plugins that are currently available on the QIIME 2 plugin
availability page. The future plugins page lists plugins that are being
developed.
This package provides templates for QIIME 2 plugins.
Please cite:
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso:
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
(eprint)
Nature Biotechnology
37
(2019)
|
|
r-bioc-annotationhub
GNU R client to access AnnotationHub resources
|
Versions of package r-bioc-annotationhub |
Release | Version | Architectures |
trixie | 3.12.0+dfsg-1 | all |
buster | 2.14.3+dfsg-1 | all |
bullseye | 2.22.0+dfsg-1 | all |
bookworm | 3.6.0+dfsg-1 | all |
stretch | 2.6.4-1 | all |
experimental | 3.14.0+dfsg-1 | all |
sid | 3.12.0+dfsg-1 | all |
upstream | 3.14.0 |
|
License: DFSG free
|
This package provides a client for the Bioconductor AnnotationHub web
resource. The AnnotationHub web resource provides a central location
where genomic files (e.g., VCF, bed, wig) and other resources from
standard locations (e.g., UCSC, Ensembl) can be discovered. The resource
includes metadata about each resource, e.g., a textual description,
tags, and date of modification. The client creates and manages a local
cache of files retrieved by the user, helping with quick and
reproducible access.
|
|
r-bioc-aroma.light
BioConductor methods normalization and visualization of microarray data
|
Versions of package r-bioc-aroma.light |
Release | Version | Architectures |
buster | 3.12.0-1 | all |
trixie | 3.34.0-1 | all |
experimental | 3.36.0-1 | all |
stretch | 3.4.0-1 | all |
sid | 3.34.0-1 | all |
bullseye | 3.20.0-1 | all |
bookworm | 3.28.0-1 | all |
upstream | 3.36.0 |
|
License: DFSG free
|
This BioConductor module provides light-weight methods for
normalization and visualization of microarray data using only basic R
data types.
Methods for microarray analysis that take basic data types such as
matrices and lists of vectors. These methods can be used standalone, be
utilized in other packages, or be wrapped up in higher-level classes.
|
|
r-bioc-beachmat
I/O for several formats storing matrix data
|
Versions of package r-bioc-beachmat |
Release | Version | Architectures |
sid | 2.20.0+ds-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bullseye | 2.6.4+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.14.0+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.20.0+ds-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
upstream | 2.22.0 |
|
License: DFSG free
|
Provides a consistent C++ class interface for reading from and
writing data to a variety of commonly used matrix types. Ordinary
matrices and several sparse/dense Matrix classes are directly supported,
third-party S4 classes may be supported by external linkage, while all
other matrices are handled by DelayedArray block processing.
|
|
r-bioc-biocneighbors
Nearest Neighbor Detection for Bioconductor Packages
|
Versions of package r-bioc-biocneighbors |
Release | Version | Architectures |
bookworm | 1.16.0+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.8.2+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.22.0+ds-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
trixie | 1.22.0+ds-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
upstream | 2.0.1 |
|
License: DFSG free
|
Implements exact and approximate methods for nearest neighbor
detection, in a framework that allows them to be easily switched within
Bioconductor packages or workflows. Exact searches can be performed using
the k-means for k-nearest neighbors algorithm or with vantage point trees.
Approximate searches can be performed using the Annoy or HNSW libraries.
Searching on either Euclidean or Manhattan distances is supported.
Parallelization is achieved for all methods by using BiocParallel. Functions
are also provided to search for all neighbors within a given distance.
|
|
r-bioc-biocsingular
Singular Value Decomposition for Bioconductor Packages
|
Versions of package r-bioc-biocsingular |
Release | Version | Architectures |
trixie | 1.20.0+ds-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
sid | 1.20.0+ds-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.14.0+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.6.0+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 1.22.0 |
|
License: DFSG free
|
Implements exact and approximate methods for singular value
decomposition and principal components analysis, in a framework that
allows them to be easily switched within Bioconductor packages or
workflows. Where possible, parallelization is achieved using
the BiocParallel framework.
|
|
r-bioc-ctc
Cluster and Tree Conversion
|
Versions of package r-bioc-ctc |
Release | Version | Architectures |
bullseye | 1.64.0-1 | all |
bookworm | 1.72.0-1 | all |
experimental | 1.80.0-1 | all |
trixie | 1.78.0-1 | all |
sid | 1.78.0-1 | all |
upstream | 1.80.0 |
|
License: DFSG free
|
Tools for export and import classification trees and clusters to other
programs.
|
|
r-bioc-dnacopy
R package: DNA copy number data analysis
|
Versions of package r-bioc-dnacopy |
Release | Version | Architectures |
trixie | 1.78.0-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.72.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.56.0-1 | amd64,arm64,armhf,i386 |
experimental | 1.80.0-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
sid | 1.78.0-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.64.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.48.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
upstream | 1.80.0 |
|
License: DFSG free
|
Implements the circular binary segmentation (CBS) algorithm to segment DNA
copy number data and identify genomic regions with abnormal copy number.
This package is for analyzing array DNA copy number data, which is usually
(but not always) called array Comparative Genomic Hybridization (array CGH)
data It implements a methodology for finding change-points in these data which
are points after which the (log) test over reference ratios have changed
location. This model is that the change-points correspond to positions where
the underlying DNA copy number has changed. Therefore, change-points can be
used to identify regions of gained and lost copy number. Also provided is a
function for making relevant plots of these data.
|
|
r-bioc-ensembldb
GNU R utilities to create and use an Ensembl based annotation database
|
Versions of package r-bioc-ensembldb |
Release | Version | Architectures |
stretch | 1.6.2-1 | all |
bullseye | 2.14.0+dfsg-1 | all |
bookworm | 2.22.0+dfsg-1 | all |
trixie | 2.28.1+dfsg-1 | all |
sid | 2.28.1+dfsg-1 | all |
buster | 2.6.5+dfsg-1 | all |
experimental | 2.30.0+dfsg-1 | all |
upstream | 2.30.0 |
|
License: DFSG free
|
The package provides functions to create and use transcript centric
annotation databases/packages. The annotation for the databases are
directly fetched from Ensembl using their Perl API. The functionality
and data is similar to that of the TxDb packages from the
GenomicFeatures package, but, in addition to retrieve all
gene/transcript models and annotations from the database, the ensembldb
package provides also a filter framework allowing to retrieve
annotations for specific entries like genes encoded on a chromosome
region or transcript models of lincRNA genes.
|
|
r-bioc-experimenthub
BioConductor client to access ExperimentHub resources
|
Versions of package r-bioc-experimenthub |
Release | Version | Architectures |
experimental | 2.14.0+ds-1 | all |
bookworm | 2.6.0+ds-1 | all |
sid | 2.12.0+ds-1 | all |
trixie | 2.12.0+ds-1 | all |
bullseye | 1.16.0+ds-1 | all |
upstream | 2.14.0 |
|
License: DFSG free
|
This package provides a client for the Bioconductor ExperimentHub web
resource. ExperimentHub provides a central location where curated data
from experiments, publications or training courses can be accessed. Each
resource has associated metadata, tags and date of modification. The
client creates and manages a local cache of files retrieved enabling
quick and reproducible access.
|
|
r-bioc-geneplotter
R package of functions for plotting genomic data
|
Versions of package r-bioc-geneplotter |
Release | Version | Architectures |
bullseye | 1.68.0-1 | all |
sid | 1.82.0+dfsg-1 | all |
stretch | 1.52.0-2 | all |
trixie | 1.82.0+dfsg-1 | all |
bookworm | 1.76.0-1 | all |
experimental | 1.84.0+dfsg-1 | all |
buster | 1.60.0-1 | all |
upstream | 1.84.0 |
|
License: DFSG free
|
Geneplotter contains plotting functions for microarrays.
The functions cPlot and cColor allow the user to
associate microarray expression data with chromosomal location.
The plots can include any subset (by default all chromosomes are
shown) of chromosomes for the organism being considered.
|
|
r-bioc-genomicalignments
BioConductor representation and manipulation of short genomic alignments
|
Versions of package r-bioc-genomicalignments |
Release | Version | Architectures |
experimental | 1.42.0-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
trixie | 1.40.0-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
sid | 1.40.0-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
stretch | 1.10.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.18.1-1 | amd64,arm64,armhf,i386 |
bullseye | 1.26.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.34.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.0.6-1 | amd64,armel,armhf,i386 |
upstream | 1.42.0 |
|
License: DFSG free
|
This BioConductor package provides efficient containers for storing and
manipulating short genomic alignments (typically obtained by aligning
short reads to a reference genome). This includes read counting,
computing the coverage, junction detection, and working with the
nucleotide content of the alignments.
|
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r-bioc-genomicfiles
Distributed computing by file or by range
|
Versions of package r-bioc-genomicfiles |
Release | Version | Architectures |
trixie | 1.40.0+dfsg-1 | all |
experimental | 1.42.0+dfsg-1 | all |
bookworm | 1.34.0-1 | all |
sid | 1.40.0+dfsg-1 | all |
bullseye | 1.26.0-1 | all |
upstream | 1.42.0 |
|
License: DFSG free
|
This package provides infrastructure for parallel
computations distributed 'by file' or 'by range'. User
defined MAPPER and REDUCER functions provide added
flexibility for data combination and manipulation.
|
|
r-bioc-genomicranges
BioConductor representation and manipulation of genomic intervals
|
Versions of package r-bioc-genomicranges |
Release | Version | Architectures |
jessie | 1.16.4-2 | amd64,armel,armhf,i386 |
bookworm | 1.50.2+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.56.2+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
buster | 1.34.0+dfsg-1 | amd64,arm64,armhf,i386 |
trixie | 1.56.1+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.42.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.26.2-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
experimental | 1.58.0+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
upstream | 1.58.0 |
|
License: DFSG free
|
The ability to efficiently store genomic annotations and alignments is
playing a central role when it comes to analyze high-throughput
sequencing data (a.k.a. NGS data). The package defines general purpose
containers for storing genomic intervals as well as more specialized
containers for storing alignments against a reference genome.
|
|
r-bioc-go.db
annotation maps describing the entire Gene Ontology
|
Versions of package r-bioc-go.db |
Release | Version | Architectures |
bullseye | 3.12.1-1 | all |
stretch | 3.4.0-1 | all |
sid | 3.19.1-1 | all |
bookworm | 3.16.0-1 | all |
trixie | 3.19.1-1 | all |
experimental | 3.20.0-1 | all |
buster | 3.7.0-1 | all |
upstream | 3.20.0 |
|
License: DFSG free
|
This package is part of BioConductor and provides a set of annotation
maps describing the entire Gene Ontology assembled using data from GO.
The package helps running the test suites of some BioConductor packages.
|
|
r-bioc-grohmm
GRO-seq Analysis Pipeline
|
Versions of package r-bioc-grohmm |
Release | Version | Architectures |
sid | 1.38.0-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
trixie | 1.38.0-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.24.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
experimental | 1.38.0-2 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.32.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 1.40.3 |
|
License: DFSG free
|
This BioConductor package provides a pipeline for the analysis of GRO-
seq data. Among the more advanced features, r-bioc-grohmm predicts the
boundaries of transcriptional activity across the genome de novo using a
two-state hidden Markov model (HMM).
The used model essentially divides the genome into transcribed and non-
transcribed regions in a strand specific manner. HMMs are used to
identify the leading edge of Pol II at genes activated by a stimulus in
GRO-seq time course data. This approach allows the genome-wide
interrogation of transcription rates in cells.
|
|
r-bioc-gviz
Plotting data and annotation information along genomic coordinates
|
Versions of package r-bioc-gviz |
Release | Version | Architectures |
stretch | 1.18.1-1 | all |
jessie | 1.8.4-1 | all |
trixie | 1.48.0+dfsg-1 | all |
bullseye | 1.34.0+dfsg-1 | all |
bookworm | 1.42.1+dfsg-1 | all |
sid | 1.48.0+dfsg-1 | all |
buster | 1.26.4-1 | all |
experimental | 1.50.0+dfsg-1 | all |
upstream | 1.50.0 |
|
License: DFSG free
|
Genomic data analyses requires integrated visualization of known
genomic information and new experimental data. Gviz uses the biomaRt and
the rtracklayer packages to perform live annotation queries to Ensembl
and UCSC and translates this to e.g. gene/transcript structures in
viewports of the grid graphics package. This results in genomic
information plotted together with your data.
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r-bioc-isoformswitchanalyzer
Identify, Annotate and Visualize Alternative Splicing and
|
Versions of package r-bioc-isoformswitchanalyzer |
Release | Version | Architectures |
bookworm | 1.20.0+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.4.0+ds-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
experimental | 2.6.0+ds-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
upstream | 2.6.0 |
|
License: DFSG free
|
Isoform Switches with Functional Consequences from both short- and
long-read RNA-seq data. Analysis of alternative splicing and
isoform switches with predicted functional consequences (e.g.
gain/loss of protein domains etc.) from quantification of all
types of RNASeq by tools such as Kallisto, Salmon, StringTie,
Cufflinks/Cuffdiff etc.
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r-bioc-org.hs.eg.db
genome-wide annotation for Human
|
Versions of package r-bioc-org.hs.eg.db |
Release | Version | Architectures |
bullseye | 3.12.0-1 | all |
experimental | 3.20.0-1 | all |
sid | 3.19.1-1 | all |
trixie | 3.19.1-1 | all |
bookworm | 3.16.0-1 | all |
upstream | 3.20.0 |
|
License: DFSG free
|
This package provides descriptions of parts of the human genome
that have been identified to be coding for RNA, and likely also for
proteins. It also offers links to entries of equivalent (orthologous)
genes in other species.
This package is prepared from the BioConductor community and contributes
to many workflows and routine analyses in computational biology.
|
|
r-bioc-qusage
qusage: Quantitative Set Analysis for Gene Expression
|
Versions of package r-bioc-qusage |
Release | Version | Architectures |
experimental | 2.40.0-1 | all |
sid | 2.38.0-1 | all |
bullseye | 2.24.0-1 | all |
trixie | 2.38.0-1 | all |
bookworm | 2.32.0-1 | all |
upstream | 2.40.0 |
|
License: DFSG free
|
This package is an implementation the Quantitative Set
Analysis for Gene Expression (QuSAGE) method described in
(Yaari G. et al, Nucl Acids Res, 2013). This is a novel Gene
Set Enrichment-type test, which is designed to provide a
faster, more accurate, and easier to understand test for gene
expression studies. qusage accounts for inter-gene correlations
using the Variance Inflation Factor technique proposed by Wu et
al. (Nucleic Acids Res, 2012). In addition, rather than simply
evaluating the deviation from a null hypothesis with a single
number (a P value), qusage quantifies gene set activity with a
complete probability density function (PDF). From this PDF, P
values and confidence intervals can be easily extracted.
Preserving the PDF also allows for post-hoc analysis (e.g.,
pair-wise comparisons of gene set activity) while maintaining
statistical traceability. Finally, while qusage is compatible
with individual gene statistics from existing methods (e.g.,
LIMMA), a Welch-based method is implemented that is shown to
improve specificity. For questions, contact Chris Bolen
(cbolen1@gmail.com) or Steven Kleinstein
(steven.kleinstein@yale.edu)
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r-bioc-savr
GNU R parse and analyze Illumina SAV files
|
Versions of package r-bioc-savr |
Release | Version | Architectures |
stretch | 1.12.0-1 | all |
sid | 1.37.0-4 | all |
trixie | 1.37.0-4 | all |
buster | 1.20.0-1 | all |
bullseye | 1.28.0-1 | all |
bookworm | 1.36.0-2 | all |
|
License: DFSG free
|
This BioConductor module enables to parse Illumina Sequence Analysis
Viewer (SAV) files, access data, and generate QC plots.
|
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r-bioc-singlecellexperiment
S4 Classes for Single Cell Data
|
Versions of package r-bioc-singlecellexperiment |
Release | Version | Architectures |
trixie | 1.26.0+ds-1 | all |
bullseye | 1.12.0+ds-1 | all |
experimental | 1.28.1+ds-1 | all |
bookworm | 1.20.0+ds-1 | all |
sid | 1.26.0+ds-1 | all |
upstream | 1.28.1 |
|
License: DFSG free
|
Defines a S4 class for storing data from single-cell
experiments. This includes specialized methods to store and
retrieve spike-in information, dimensionality reduction
coordinates and size factors for each cell, along with the
usual metadata for genes and libraries.
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r-bioc-structuralvariantannotation
Variant annotations for structural variants
|
Versions of package r-bioc-structuralvariantannotation |
Release | Version | Architectures |
bookworm | 1.13.0+ds-1 | all |
trixie | 1.20.0+ds-1 | all |
experimental | 1.22.0+ds-1 | all |
sid | 1.20.0+ds-1 | all |
upstream | 1.22.0 |
|
License: DFSG free
|
StructuralVariantAnnotation contains useful helper
functions for dealing with structural variants in VCF format.
The packages contains functions for parsing VCFs from a number
of popular callers as well as functions for dealing with
breakpoints involving two separate genomic loci encoded as
GRanges objects.
|
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r-bioc-tximport
transcript-level estimates for biological sequencing
|
Versions of package r-bioc-tximport |
Release | Version | Architectures |
bookworm | 1.26.1+dfsg-1 | all |
trixie | 1.32.0+dfsg-1 | all |
sid | 1.32.0+dfsg-1 | all |
bullseye | 1.18.0+dfsg-1 | all |
experimental | 1.34.0+dfsg-1 | all |
upstream | 1.34.0 |
|
License: DFSG free
|
Imports transcript-level abundance, estimated counts and
transcript lengths, and summarizes into matrices for use with
downstream gene-level analysis packages. Average transcript
length, weighted by sample-specific transcript abundance
estimates, is provided as a matrix which can be used as an
offset for different expression of gene-level counts.
|
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r-cran-amap
Another Multidimensional Analysis Package
|
Versions of package r-cran-amap |
Release | Version | Architectures |
bookworm | 0.8-19-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.8-20-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.8-19-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.8-18-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
Tools for Clustering and Principal Component Analysis
(With robust methods, and parallelized functions).
|
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r-cran-biwt
biweight mean vector and covariance and correlation
|
Versions of package r-cran-biwt |
Release | Version | Architectures |
bullseye | 1.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.0.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.0.1-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.0.1-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
Compute multivariate location, scale, and correlation
estimates based on Tukey's biweight M-estimator.
|
|
r-cran-boolnet
assembling, analyzing and visualizing Boolean networks
|
Versions of package r-cran-boolnet |
Release | Version | Architectures |
stretch | 2.1.3-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.1.4-1 | amd64,arm64,armhf,i386 |
bullseye | 2.1.5-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.1.7-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.1.9-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.1.9-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 2.0-1 | amd64,armel,armhf,i386 |
|
License: DFSG free
|
BoolNet is an R package that provides tools for assembling, analyzing and
visualizing synchronous and asynchronous Boolean networks as well as
probabilistic Boolean networks.
|
|
r-cran-corrplot
Visualization of a Correlation Matrix
|
Versions of package r-cran-corrplot |
Release | Version | Architectures |
bullseye | 0.84-3 | all |
buster-backports | 0.84-3~bpo10+1 | all |
sid | 0.94-1 | all |
trixie | 0.94-1 | all |
bookworm | 0.92-1 | all |
upstream | 0.95 |
|
License: DFSG free
|
A graphical display of a correlation matrix or general matrix.
It also contains some algorithms to do matrix reordering. In addition,
corrplot is good at details, including choosing color, text labels,
color labels, layout, etc.
|
|
r-cran-dynamictreecut
Methods for Detection of Clusters in Hierarchical Clustering
|
Versions of package r-cran-dynamictreecut |
Release | Version | Architectures |
sid | 1.63-1-3 | all |
bullseye | 1.63-1-3 | all |
trixie | 1.63-1-3 | all |
bookworm | 1.63-1-3 | all |
|
License: DFSG free
|
Dendrograms Contains methods for detection of clusters in hierarchical
clustering dendrograms.
|
|
r-cran-epir
GNU R Functions for analysing epidemiological data
|
Versions of package r-cran-epir |
Release | Version | Architectures |
bullseye | 2.0.19-1 | all |
bookworm | 2.0.57+dfsg-1 | all |
sid | 2.0.76+dfsg-1 | all |
buster | 0.9-99-1 | all |
stretch | 0.9-79-1 | all |
jessie | 0.9-59-1 | all |
trixie | 2.0.76+dfsg-1 | all |
upstream | 2.0.78 |
Debtags of package r-cran-epir: |
devel | lang:r |
field | medicine |
interface | commandline |
role | program |
use | analysing |
|
License: DFSG free
|
A package for analysing epidemiological data. Contains functions for
directly and indirectly adjusting measures of disease frequency,
quantifying measures of association on the basis of single or multiple
strata of count data presented in a contingency table, and computing
confidence intervals around incidence risk and incidence rate estimates.
Miscellaneous functions for use in meta-analysis, diagnostic test
interpretation, and sample size calculations.
|
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r-cran-fitdistrplus
support fit of parametric distribution
|
Versions of package r-cran-fitdistrplus |
Release | Version | Architectures |
trixie | 1.2-1-1 | all |
bookworm | 1.1-8-1 | all |
sid | 1.2-1-1 | all |
bullseye | 1.1-3-1 | all |
stretch-backports-sloppy | 1.1-1-1~bpo9+1 | all |
buster-backports | 1.1-3-1~bpo10+1 | all |
|
License: DFSG free
|
Extends the fitdistr() function (of the MASS package) with several
functions to help the fit of a parametric distribution to non-censored
or censored data. Censored data may contain left censored, right
censored and interval censored values, with several lower and upper
bounds. In addition to maximum likelihood estimation (MLE), the package
provides moment matching (MME), quantile matching (QME) and maximum
goodness-of-fit estimation (MGE) methods (available only for non-censored
data). Weighted versions of MLE, MME and QME are available. See
e.g. Casella & Berger (2002). Statistical inference. Pacific Grove.
|
|
r-cran-forecast
GNU R forecasting functions for time series and linear models
|
Versions of package r-cran-forecast |
Release | Version | Architectures |
bullseye | 8.13-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 8.20-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 8.23.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 8.23.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
Methods and tools for displaying and analysing
univariate time series forecasts including exponential smoothing
via state space models and automatic ARIMA modelling.
|
|
r-cran-gprofiler2
Interface to the 'g:Profiler' Toolset
|
Versions of package r-cran-gprofiler2 |
Release | Version | Architectures |
sid | 0.2.3+dfsg-1 | all |
trixie | 0.2.3+dfsg-1 | all |
bookworm | 0.2.1+dfsg-1 | all |
|
License: DFSG free
|
A toolset for functional enrichment analysis and visualization,
gene/protein/SNP identifier conversion and mapping orthologous genes
across species via 'g:Profiler' (https://biit.cs.ut.ee/gprofiler). The
main tools are:
(1) 'g:GOSt' - functional enrichment analysis and visualization of
gene lists;
(2) 'g:Convert' - gene/protein/transcript identifier conversion across
various namespaces;
(3) 'g:Orth' - orthology search across species;
(4) 'g:SNPense' - mapping SNP rs identifiers to chromosome positions,
genes and variant effects This package is an R interface
corresponding to the 2019 update of 'g:Profiler' and provides access
to 'g:Profiler' for versions 'e94_eg41_p11' and higher. See the
package 'gProfileR' for accessing older versions from the
'g:Profiler' toolset.
|
|
r-cran-minerva
Maximal Information-Based Nonparametric Exploration
|
Versions of package r-cran-minerva |
Release | Version | Architectures |
sid | 1.5.10-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.5.10-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.5.10-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.5.8-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
Wrapper for 'minepy' implementation of Maximal
Information-based Nonparametric Exploration statistics (MIC and
MINE family). Detailed information of the ANSI C implementation of
'minepy' can be found at http://minepy.readthedocs.io/en/latest.
|
|
r-cran-optimalcutpoints
Computing Optimal Cutpoints in Diagnostic Tests
|
Versions of package r-cran-optimalcutpoints |
Release | Version | Architectures |
bullseye | 1.1-4-2 | all |
trixie | 1.1-5-1 | all |
sid | 1.1-5-1 | all |
bookworm | 1.1-5-1 | all |
|
License: DFSG free
|
Computes optimal cutpoints for diagnostic tests or continuous markers.
Various approaches for selecting optimal cutoffs have been implemented,
including methods based on cost-benefit analysis and diagnostic test
accuracy measures (Sensitivity/Specificity, Predictive Values and
Diagnostic Likelihood Ratios). Numerical and graphical output for all
methods is easily obtained.
|
|
r-cran-parmigene
Parallel Mutual Information to establish Gene Networks
|
Versions of package r-cran-parmigene |
Release | Version | Architectures |
sid | 1.1.1-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.1.1-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.1.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.1.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
The package provides a parallel estimation of the mutual
information based on entropy estimates from k-nearest neighbors
distances and algorithms for the reconstruction of gene
regulatory networks.
|
|
r-cran-pheatmap
GNU R package to create pretty heatmaps
|
Versions of package r-cran-pheatmap |
Release | Version | Architectures |
bookworm | 1.0.12-2 | all |
trixie | 1.0.12-2 | all |
sid | 1.0.12-2 | all |
stretch | 1.0.8-1 | all |
buster | 1.0.12-1 | all |
bullseye | 1.0.12-2 | all |
|
License: DFSG free
|
GNU R implementation of heatmaps that offers more control over dimensions and
appearance.
|
|
r-cran-qqman
R package for visualizing GWAS results using Q-Q and manhattan plots
|
Versions of package r-cran-qqman |
Release | Version | Architectures |
stretch | 0.1.2-1 | all |
sid | 0.1.9+dfsg-1 | all |
trixie | 0.1.9+dfsg-1 | all |
bookworm | 0.1.8+dfsg-1 | all |
buster | 0.1.4-6 | all |
bullseye | 0.1.4-7 | all |
|
License: DFSG free
|
qqman is an add-on package for the R statistical environment. This package
provides functions for visualizing Genome-Wide Association Studies (GWAS)
results using Manhattan plots and Quantile-Quantile plots.
|
|
r-cran-rcpphnsw
R bindings for a Library for Approximate Nearest Neighbors
|
Versions of package r-cran-rcpphnsw |
Release | Version | Architectures |
trixie | 0.5.0+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.5.0+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.4.1+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.3.0.9001+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 0.6.0 |
|
License: DFSG free
|
'Hnswlib' is a C++ library for Approximate Nearest Neighbors. This
package provides a minimal R interface by relying on the 'Rcpp' package. See
https://github.com/nmslib/hnswlib for more on 'hnswlib'. 'hnswlib' is
released under Version 2.0 of the Apache License.
|
|
r-cran-rentrez
GNU R interface to the NCBI's EUtils API
|
Versions of package r-cran-rentrez |
Release | Version | Architectures |
sid | 1.2.3+dfsg-1 | all |
stretch | 1.0.4-1 | all |
bullseye | 1.2.3+dfsg-1 | all |
buster | 1.2.1-2 | all |
bookworm | 1.2.3+dfsg-1 | all |
trixie | 1.2.3+dfsg-1 | all |
|
License: DFSG free
|
Provides an R interface to the NCBI's EUtils API allowing users to
search databases like GenBank and PubMed, process the results of those
searches and pull data into their R sessions.
|
|
r-cran-sctransform
Variance Stabilizing Transformations for Single Cell UMI Data
|
Versions of package r-cran-sctransform |
Release | Version | Architectures |
trixie | 0.4.1-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.3.5-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.3.2-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.4.1-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
A normalization method for single-cell UMI count data using a
variance stabilizing transformation. The transformation is based on a
negative binomial regression model with regularized parameters. As part of the
same regression framework, this package also provides functions for
batch correction, and data correction. See Hafemeister and Satija 2019
for more details.
|
|
resfinder-db
ResFinder database is a curated database of acquired resistance genes
|
Versions of package resfinder-db |
Release | Version | Architectures |
bullseye | 0.0+git20200408.0322c0d-1 | all |
trixie | 0.0+git20220524.fa32d9a-1 | all |
bookworm | 0.0+git20220524.fa32d9a-1 | all |
sid | 0.0+git20220524.fa32d9a-1 | all |
upstream | 0.0+git20241213.d3b2312 |
|
License: DFSG free
|
ResFinder identifies acquired antimicrobial resistance genes in total or
partial sequenced isolates of bacteria.
ResFinder that uses BLAST for identification of acquired antimicrobial
resistance genes in whole-genome data. As input, the method can use both
pre-assembled, complete or partial genomes, and short sequence reads
from four different sequencing platforms. The method was evaluated on
1862 GenBank files containing 1411 different resistance genes, as well
as on 23 de-novo-sequenced isolates.
This package provides the database needed for resfinder.
|
|
science-workflow
workflow management systems useful for scientific research
|
Versions of package science-workflow |
Release | Version | Architectures |
stretch | 1.7 | all |
bullseye | 1.14.2 | all |
buster | 1.10 | all |
bookworm | 1.14.5 | all |
sid | 1.14.7 | all |
trixie | 1.14.7 | all |
|
License: DFSG free
|
This task lists some packages providing workflow management
systems useful for scientific research.
|
|
Debian packages in contrib or non-free
arb
phylogenetic sequence analysis suite - main program
|
Versions of package arb |
Release | Version | Architectures |
bookworm | 6.0.6-5 (non-free) | amd64,i386 |
sid | 6.0.6-8 (non-free) | amd64,arm64,armel,armhf,i386,mips64el,riscv64,s390x |
bullseye | 6.0.6-4 (non-free) | amd64,i386 |
buster | 6.0.6-4 (non-free) | amd64,i386 |
trixie | 6.0.6-8 (non-free) | amd64,arm64,armel,armhf,i386,mips64el,riscv64,s390x |
jessie | 6.0.2-1+deb8u1 (non-free) | amd64,i386 |
stretch | 6.0.6-1 (non-free) | amd64,i386 |
upstream | 7.0 |
Debtags of package arb: |
field | biology |
role | program |
uitoolkit | motif |
x11 | application |
|
License: non-free
|
ARB is a graphical suite of tools for sequence database handling and data
analysis. A central database of processed (aligned) sequences and any
type of additional data linked to the sequence entries is structured
according to phylogeny or other user-defined criteria.
The ARB project (from the Latin "arbor", a tree) is a joint initiative of
the Lehrstuhl für Mikrobiologie and the LRR of the Technische Universität
München in 1992.
Since 2014 the ARB project is continued by the Department of Molecular
Ecology http://www.mpi-bremen.de/en/Department_of_Molecular_Ecology.html
at the Max Planck Institute for Marine Microbiology in Bremen in
cooperation with Ribocon GmbH http://www.ribocon.com .
|
bcbio
toolkit for analysing high-throughput sequencing data
|
Versions of package bcbio |
Release | Version | Architectures |
bullseye | 1.2.5-1 (contrib) | all |
buster | 1.1.2-3 | all |
bookworm | 1.2.9-2 (contrib) | all |
sid | 1.2.9-2 (contrib) | all |
|
License: DFSG free, but needs non-free components
|
This package installs the command line tools of the bcbio-nextgen
toolkit implementing best-practice pipelines for fully automated high
throughput sequencing analysis.
A high-level configuration file specifies inputs and analysis parameters
to drive a parallel pipeline that handles distributed execution,
idempotent processing restarts and safe transactional steps. The project
contributes a shared community resource that handles the data processing
component of sequencing analysis, providing researchers with more time
to focus on the downstream biology.
This package builds and having it in Debian unstable helps the Debian
developers to synchronize their efforts. But unless a series of external
dependencies are not installed manually, the functionality of bcbio in
Debian is only a shadow of itself. Please use the official distribution
of bcbio for the time being, which means "use conda". The TODO file in
the Debian directory should give an overview on progress for Debian
packaging.
|
blimps-utils
blocks database improved searcher
|
Versions of package blimps-utils |
Release | Version | Architectures |
sid | 3.9+ds-3 (non-free) | amd64 |
stretch | 3.9-1 (non-free) | amd64 |
buster | 3.9+ds-1 (non-free) | amd64 |
jessie | 3.9-1 (non-free) | amd64 |
trixie | 3.9+ds-3 (non-free) | amd64 |
bookworm | 3.9+ds-1 (non-free) | amd64 |
bullseye | 3.9+ds-1 (non-free) | amd64 |
|
License: non-free
|
BLIMPS (BLocks IMProved Searcher) is a searching tool that scores
a protein sequence against blocks or a block against sequences.
This package contains the binaries.
|
caftools
maintenance of DNA sequence assemblies
|
Versions of package caftools |
Release | Version | Architectures |
bullseye | 2.0.3-1 (non-free) | amd64 |
|
License: non-free
|
This package contains code from different authors that allow sequence
assemblies to be converted into formats such as CAF (Common Assembly
Format) or GAP4.
CAF is a text format for describing sequence assemblies. It
is acedb-compliant and is an extension of the ace-file format used
earlier, but with support for base quality measures and a more extensive
description of the Sequence data. CAF was designed during the Sanger
sequencing era. Its modern-day successor is the SAM format, or its
binary equivalents BAM and CRAM.
|
cluster3
Reimplementation of the Eisen-clustering software
|
Versions of package cluster3 |
Release | Version | Architectures |
bullseye | 1.59+ds-3 (non-free) | amd64 |
trixie | 1.59+ds-6 (non-free) | amd64 |
jessie | 1.52a-1 (non-free) | amd64 |
stretch | 1.52a-1 (non-free) | amd64 |
buster | 1.57-1 (non-free) | amd64 |
sid | 1.59+ds-6 (non-free) | amd64 |
bookworm | 1.59+ds-5 (non-free) | amd64 |
|
License: non-free
|
The open source clustering software available here contains clustering
routines that can be used to analyze gene expression data. Routines for
hierarchical (pairwise simple, complete, average, and centroid linkage)
clustering, k-means and k-medians clustering, and 2D self-organizing maps
are included. The routines are available in the form of a C clustering
library, an extension module to Python, a module to Perl, as well as an
enhanced version of Cluster, which was originally developed by Michael
Eisen of Berkeley Lab. The C clustering library and the associated
extension module for Python was released under the Python license. The
Perl module was released under the Artistic License. Cluster 3.0 is
covered by the original Cluster/TreeView license.
This package only contains the command line and motif gui versions
of Cluster 3.0.
|
cufflinks
Transcript assembly, differential expression and regulation for RNA-Seq
|
Versions of package cufflinks |
Release | Version | Architectures |
jessie | 2.2.1-1 (non-free) | amd64 |
stretch | 2.2.1-3 (non-free) | amd64 |
bullseye | 2.2.1+dfsg.1-8 (non-free) | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.2.1+dfsg.1-9 (non-free) | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.2.1+dfsg.1-10 (non-free) | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.2.1+dfsg.1-10 (non-free) | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 2.2.1+dfsg.1-3 (non-free) | amd64,arm64,armhf,i386 |
|
License: non-free
|
Cufflinks assembles transcripts, estimates their abundances, and
tests for differential expression and regulation in RNA-Seq samples.
It accepts aligned RNA-Seq reads and assembles the alignments into a
parsimonious set of transcripts. Cufflinks then estimates the
relative abundances of these transcripts based on how many reads
support each one.
This package provides the binary of cufflinks and associated tools, i.e.
compress_gtf, cuffcompare, cuffdiff, cuffmerge, cuffnorm, cuffquant and
gtf_to_sam.
|
embassy-phylip
EMBOSS conversions of the programs in the phylip package
|
Versions of package embassy-phylip |
Release | Version | Architectures |
stretch | 3.69.660-1 (non-free) | amd64 |
buster | 3.69.660-3 (non-free) | amd64 |
jessie | 3.69.650-2 (non-free) | amd64 |
|
License: non-free
|
This package is the adaptation of the PHYLIP package in which its
programs can operate with the biological sequence formats and databases
of the European Molecular Biology Open Software Suite (EMBOSS). The
software packages adapted for EMBOSS are called EMBASSY.
PHYLIP (the PHYLogeny Inference Package) is a package of programs for
inferring phylogenies (evolutionary trees). Methods that are available
in the package include parsimony, distance matrix, and likelihood
methods, including bootstrapping and consensus trees. Data types that
can be handled include molecular sequences, gene frequencies,
restriction sites and fragments, distance matrices, and discrete
characters.
The EMBASSY PHYLIP programs all have the prefix "f" to distinguish them
from the original programs and avoid namespace conflict.
|
relion-cuda
parallel toolkit for 3D reconstructions in cryo-electron microscopy
|
Versions of package relion-cuda |
Release | Version | Architectures |
bullseye | 3.1.0-2 (contrib) | amd64 |
bookworm | 3.1.3-2 (contrib) | amd64 |
sid | 3.1.3-2 (contrib) | amd64 |
upstream | 5.0.0 |
|
License: DFSG free, but needs non-free components
|
RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone
computer program for Maximum A Posteriori refinement of (multiple) 3D
reconstructions or 2D class averages in cryo-electron microscopy.
RELION provides a GUI, several command-line tools in parallel (MPI) and serial
versions, optionally with CUDA/GPU support.
relion-cuda provides the serial and parallel (MPI) command-line tools with
CUDA/GPU support.
|
relion-gui-cuda
toolkit for 3D reconstructions in cryo-electron microscopy (gui apps)
|
Versions of package relion-gui-cuda |
Release | Version | Architectures |
bullseye | 3.1.0-2 (contrib) | amd64 |
bookworm | 3.1.3-2 (contrib) | amd64 |
sid | 3.1.3-2 (contrib) | amd64 |
upstream | 5.0.0 |
|
License: DFSG free, but needs non-free components
|
RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone
computer program for Maximum A Posteriori refinement of (multiple) 3D
reconstructions or 2D class averages in cryo-electron microscopy.
RELION provides a GUI, several command-line tools in parallel (MPI) and serial
versions, optionally with CUDA/GPU support.
relion-gui-cuda provides the graphical user interface with CUDA/GPU support.
|
seq-gen
simulate the evolution of nucleotide or amino acid sequences
|
Versions of package seq-gen |
Release | Version | Architectures |
sid | 1.3.4-2 (non-free) | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.3.4-2 (non-free) | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.3.4-2 (non-free) | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.3.4-2 (non-free) | amd64,arm64,armhf,i386 |
stretch | 1.3.3-1 (non-free) | amd64,armel,armhf,i386,mips,mipsel,s390x |
jessie | 1.3.3-1 (non-free) | amd64,armel,armhf,i386 |
trixie | 1.3.4-2 (non-free) | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package seq-gen: |
role | program |
|
License: non-free
|
Seq-Gen is a program that will simulate the evolution of nucleotide
or amino acid sequences along a phylogeny, using common models of the
substitution process. A range of models of molecular evolution are
implemented including the general reversible model. State frequencies
and other parameters of the model may be given and site-specific rate
heterogeneity may also be incorporated in a number of ways. Any number
of trees may be read in and the program will produce any number of data
sets for each tree. Thus large sets of replicate simulations can be
easily created. It has been designed to be a general purpose simulator
that incorporates most of the commonly used
(and computationally tractable) models of molecular sequence evolution.
|
seqcluster
analysis of small RNA in NGS data
|
Versions of package seqcluster |
Release | Version | Architectures |
bullseye | 1.2.7+ds-1 (contrib) | all |
bookworm | 1.2.9+ds-3 (contrib) | all |
trixie | 1.2.9+ds-4 (contrib) | all |
sid | 1.2.9+ds-4 (contrib) | all |
|
License: DFSG free, but needs non-free components
|
Seqcluster investigates small RNA sequences of all sorts in RNA
sequencing data. This is especially helpful for the identification of
RNA that is neither coding nor belonging to the already well-established
group of miRNA, towards many tools feel constrained to.
|
sift
predicts if a substitution in a protein has a phenotypic effect
|
Versions of package sift |
Release | Version | Architectures |
jessie | 4.0.3b-4 (non-free) | amd64 |
stretch | 4.0.3b-4 (non-free) | amd64 |
buster | 4.0.3b-6 (non-free) | amd64 |
bullseye | 4.0.3b-6 (non-free) | amd64 |
bookworm | 4.0.3b-6 (non-free) | amd64 |
sid | 4.0.3b-6 (non-free) | amd64 |
|
License: non-free
|
SIFT is a sequence homology-based tool that sorts intolerant from tolerant
amino acid substitutions and predicts whether an amino acid substitution
in a protein will have a phenotypic effect. SIFT is based on the premise
that protein evolution is correlated with protein function. Positions
important for function should be conserved in an alignment of the protein
family, whereas unimportant positions should appear diverse in an alignment.
|
solvate
arranges water molecules around protein structures
|
Versions of package solvate |
Release | Version | Architectures |
trixie | 1.0-3 (non-free) | amd64 |
buster | 1.0-2 (non-free) | amd64 |
bullseye | 1.0-3 (non-free) | amd64 |
bookworm | 1.0-3 (non-free) | amd64 |
sid | 1.0-3 (non-free) | amd64 |
|
License: non-free
|
For molecular dynamics simulations it is sometimes appropriate
not to model in the vacuum but to have the proteins surrounded
by their solvent. This program computes the location of water
molecules such that the resulting PDB files become suitable
for further analyses.
|
trnascan-se
detection of transfer RNA genes in genomic sequence
|
Versions of package trnascan-se |
Release | Version | Architectures |
bullseye | 2.0.7+ds-1 (non-free) | amd64,i386 |
buster | 2.0.0-3 (non-free) | amd64 |
bookworm | 2.0.10+ds-1 (non-free) | amd64,i386 |
trixie | 2.0.12+ds-1 (non-free) | amd64,arm64,i386 |
sid | 2.0.12+ds-1 (non-free) | amd64,arm64,i386 |
|
License: non-free
|
tRNAscan-SE identifies 99-100% of transfer RNA genes in DNA sequence while
giving less than one false positive per 15 gigabases. Two previously described
tRNA detection programs are used as fast, first-pass prefilters to identify
candidate tRNAs, which are then analyzed by a highly selective tRNA covariance
model. This work represents a practical application of RNA covariance models,
which are general, probabilistic secondary structure profiles based on
stochastic context-free grammars. tRNAscan-SE searches at ~ 30 000 bp/s.
Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as
selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudogenes.
|
varscan
variant detection in next-generation sequencing data
|
Versions of package varscan |
Release | Version | Architectures |
buster | 2.4.3+dfsg-3 (non-free) | amd64 |
stretch | 2.4.3+dfsg-1 (non-free) | amd64 |
bullseye | 2.4.3+dfsg-3 (non-free) | amd64 |
jessie | 2.3.7+dfsg-1 (non-free) | amd64 |
bookworm | 2.4.3+dfsg-4 (non-free) | amd64 |
trixie | 2.4.3+dfsg-4 (non-free) | amd64 |
sid | 2.4.3+dfsg-4 (non-free) | amd64 |
|
License: non-free
|
Variant detection in massively parallel sequencing. For one sample,
calls SNPs, indels, and consensus genotypes. For tumor-normal pairs,
further classifies each variant as Germline, Somatic, or LOH, and also
detects somatic copy number changes.
|
vdjtools
framework for post-analysis of B/T cell repertoires
|
Versions of package vdjtools |
Release | Version | Architectures |
sid | 1.2.1+git20190311+repack-2 (non-free) | all |
trixie | 1.2.1+git20190311+repack-2 (non-free) | all |
bullseye | 1.2.1+git20190311-5 (non-free) | all |
bookworm | 1.2.1+git20190311+repack-1 (non-free) | all |
|
License: non-free
|
VDJtools is an open-source Java/Groovy-based framework designed
to facilitate analysis of immune repertoire sequencing (RepSeq)
data. VDJtools computes a wide set of statistics and is able to perform
various forms of cross-sample analysis. Both comprehensive tabular
output and publication-ready plots are provided.
The main aims of the VDJtools Project are:
- To ensure consistency between post-analysis methods and results
- To save the time of bioinformaticians analyzing RepSeq data
- To create an API framework facilitating development of new RepSeq
analysis applications
- To provide a simple enough command line tool so it could be used by
immunologists and biologists with little computational background
Please cite:
M Shugay, D.V. Bagaev, M.A. Turchaninova, D.A. Bolotin, O.V. Britanova, E.V. Putintseva, M.V. Pogorelyy, V.I. Nazarov VI, I.V. Zvyagin, V.I. Kirgizova, K.I. Kirgizov, E.V. Skorobogatova and D.M. Chudakov:
VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires.
(PubMed,eprint)
PLoS Comput Biol.
11(11):e1004503
(2015)
|
vienna-rna
|
Versions of package vienna-rna |
Release | Version | Architectures |
trixie | 2.6.4+dfsg-1 (non-free) | amd64,arm64,armel,armhf,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.5.1+dfsg-1 (non-free) | amd64,arm64,mips64el,ppc64el,s390x |
bullseye | 2.4.17+dfsg-2 (non-free) | amd64,arm64,armel,armhf,mips64el,mipsel,ppc64el |
sid | 2.6.4+dfsg-1 (non-free) | amd64,arm64,armel,armhf,mips64el,ppc64el,riscv64,s390x |
upstream | 2.7.0 |
|
License: non-free
|
The Vienna RNA Package consists of a C code library and several
stand-alone programs for the prediction and comparison of RNA secondary
structures. It is developed and maintained by the group of Ivo Hofacker
in Vienna.
RNA secondary structure prediction through energy minimization is the
most used function in the package. It provides three kinds of dynamic
programming algorithms for structure prediction:
- the minimum free energy algorithm of (Zuker & Stiegler 1981) which
yields a single optimal structure,
- the partition function algorithm of (McCaskill 1990) which calculates
base pair probabilities in the thermodynamic ensemble, and the
suboptimal folding algorithm of (Wuchty et.al 1999) which generates
all suboptimal structures within a given energy range of the optimal
energy.
For secondary structure comparison, the package contains several
measures of distance (dissimilarities) using either string alignment or
tree-editing (Shapiro & Zhang 1990). Finally, is provided an algorithm
to design sequences with a predefined structure (inverse folding).
The RNAforester package is a tool for aligning RNA secondary structures
and it's user interface integrates to those of the tools of the
Vienna RNA package.
Please cite:
Ronny Lorenz, Stephan H. Bernhart, Christian Höner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F. Stadler and Ivo L. Hofacker:
ViennaRNA Package 2.0.
(eprint)
Algorithms for Molecular Biology
6(1):26
(2011)
|
Debian packages in New queue (hopefully available soon)
sourmash
tools for comparing DNA sequences with MinHash sketches
|
Versions of package sourmash |
Release | Version | Architectures |
NEW | 4.8.11-1 | all |
|
License: unknown
Version: 4.8.11-1
|
Compute MinHash signatures for nucleotide (DNA/RNA) and protein sequences.
MinHash sketches provide a lightweight way to store “signatures” of large DNA
or RNA sequence collections, and then compare or search them using a Jaccard
index. MinHash sketches can be used to identify samples, find similar samples,
identify data sets with shared sequences, and build phylogenetic trees
(Ondov et al. 2015).
sourmash provides a command line script, a Python library, and a CPython
module for MinHash sketches
|
Packaging has started and developers might try the packaging code in VCS
acacia
Error-corrector for pyrosequenced amplicon reads.
|
Versions of package acacia |
Release | Version | Architectures |
VCS | 1.53-0biolinux3 | all |
|
License: GPL-3
Debian package not available
Version: 1.53-0biolinux3
|
Acacia is a java program developed to quickly and conservatively correct
errors, whilst simultaneously de-replicating, amplicon sequences.
The main purpose of Acacia is to correct the over-call, under-call errors
prevalent in Roche 454 GS-FLX data, and more recently, with the Titanium
chemistry.
Acacia will only ectively correct errors in amplicons - as it assumes that
the 5' end of the sequences start at the same position, the MID, followed by
the primer.
Acacia uses empirically-derived models to identify homopolymer
regions where there are more `errors' than expected by chance - these imply
that the differences are due to population differences rather than
error-induced polymorphisms.
Nat Methods. 2012 Apr 27;9(5):425-6. doi: 10.1038/nmeth.1990.
Fast, accurate error-correction of amplicon pyrosequences using Acacia.
Bragg L, Stone G, Imelfort M, Hugenholtz P, Tyson GW.
|
agat
another GFF analysis toolkit
|
Versions of package agat |
Release | Version | Architectures |
VCS | 0.5.0-1 | all |
|
License: GPL-3
Debian package not available
Version: 0.5.0-1
|
Suite of tools to handle gene annotations in any GTF/GFF format.
It has the power to check, fix, pad missing information
of any kind of gtf and gff to create complete, sorted and
standardised gff3 format.
|
amos-assembler
modular whole genome assembler
|
Versions of package amos-assembler |
Release | Version | Architectures |
VCS | 3.1.0-1 | all |
|
License: Artistic
Debian package not available
Version: 3.1.0-1
|
The AMOS consortium is committed to the development of open-source
whole genome assembly software. The project acronym (AMOS) represents
our primary goal - to produce A Modular, Open-Source whole genome
assembler. Open-source so that everyone is welcome to contribute and
help build outstanding assembly tools, and modular in nature so that
new contributions can be easily inserted into an existing assembly
pipeline. This modular design will foster the development of new
assembly algorithms and allow the AMOS project to continually grow
and improve in hopes of eventually becoming a widely accepted and
deployed assembly infrastructure. In this sense, AMOS is both a
design philosophy and a software system.
|
apollo
genome annotation viewer and editor
|
Versions of package apollo |
Release | Version | Architectures |
VCS | 2.3.1-1 | all |
|
License: Artistic
Debian package not available
Version: 2.3.1-1
|
Apollo is a genome annotation viewer and editor. It was developed as a
collaboration between the Berkeley Drosophila Genome Project (part of
the FlyBase consortium) and The Sanger Institute in Cambridge, UK.
Apollo allows researchers to explore genomic annotations at many levels
of detail, and to perform expert annotation curation, all in a graphical
environment. It was used by the FlyBase biologists to construct the
Release 3 annotations on the finished Drosophila melanogaster genome,
and is also a primary vehicle for sharing these annotations with the
community. The Generic Model Organism Database (GMOD) project, which
aims to provide a complete ready-to-use toolkit for analyzing whole
genomes, has adopted Apollo as its annotation workbench.
Please cite:
Susanna E. Lewis, Steve M. J. Searle, Naomi Harris, M. Gibson, V Lyer, J. Richter, C. Wiel, L. Bayraktaroglir, Ewan Birney, M. A. Crosby, J. S. Kaminker, B. B. Matthews, S. E. Prochnik, C. D. Smithy, J. L. Tupy, G. M. Rubin, S. Misra, Chris J. Mungall and Michelle E. Clamp:
Apollo: a sequence annotation editor.
(PubMed,eprint)
Genome Biology
3(12):research0082-0082.14
(2002)
|
arvados
managing and analyzing biomedical big data
|
Versions of package arvados |
Release | Version | Architectures |
VCS | 2.0.3-1 | all |
|
License: Apache-2.0 #FIXME
Debian package not available
Version: 2.0.3-1
|
Arvados is an open source platform for managing, processing, and sharing
genomic and other large scientific and biomedical data. With Arvados,
bioinformaticians run and scale compute-intensive workflows, developers
create biomedical applications, and IT administrators manage large
compute and storage resources.
|
axparafit
optimized statistical analysis of host-parasite coevolution
|
Versions of package axparafit |
Release | Version | Architectures |
VCS | 1.0-1 | all |
|
License: GPL-2+
Debian package not available
Version: 1.0-1
|
AxParafit is a highly optimized version of Pierre Legendre's Parafit program
for statistical analysis of host-parasite coevolution. AxParafit has been
parallelized with MPI (Message Passing Interface) for compute clusters and
was used to carry out the largest co-evolutionary analysis to date for the
paper describing the software.
|
axpcoords
highly optimized and parallelized porting of pcoords
|
Versions of package axpcoords |
Release | Version | Architectures |
VCS | 1.0-1 | all |
|
License: GPL-2+
Debian package not available
Version: 1.0-1
|
AxPcoords is an highly optimized versions of Pierre Legendre's DistPCoA
program for statistical analysis of host-parasite coevolution.
AxPcoords is a fast, LAPACK-based implementation of DistPCoA (see
http://www.bio.umontreal.ca/Casgrain/en/labo/distpcoa.html)
which is another program by Pierre Legendre, it conducts a principal
coordinates analysis.
This program is required for the pipeline that conducts a full host-parasite
co-phylogenetic analysis in combination with AxParafit.
|
bagpipe
|
Versions of package bagpipe |
Release | Version | Architectures |
VCS | 2012.02.15-1 | all |
|
License: GPL3+
Debian package not available
Version: 2012.02.15-1
|
Bagpipe is a program for performing genomewide linkage disequilibrium
mapping of quantitative trait loci in populations whose genome structure
can be accommodated in the HAPPY framework [Mott00]. This includes most
diploid crosses where the founders of the individuals have known genotypes.
- Bagpipe is a simplified and streamlined version of Bagphenotype that
does not currently include resample model averaging (RMA) capabilities.
- Bagpipe can help fit single locus regression models (with or without
random effects) to marker intervals whose genetic ancestry is inferred
using the HAPPY software.
- Bagpipe cannot help you decide what is a sensible model to fit.
- Bagpipe does not currently accommodate populations with significant
population structure, except through the specification of simple random
intercepts based on unpatterned covariance matrices.
- Bagpipe is named after the Scottish wind instrument "the bagpipes" and
after Bagphenotype, which in turn was a PIPEline for BAGging-based
multiple QTL analysis of phenoTYPEs. Bagphenotype was in turn based
on software written by Richard Mott and William Valdar to analyze
heterogeneous stock mice in [Valdar06].
- Bagpipe is experimental software, is provided free of charge subject to
copyleft restrictions, and comes with no guarantees whatsoever.
|
bax2bam
Convert legacy PacBio Bax.H5, Bas.H5, and Ccs.H5 files to the new PacBio BAM format
|
Versions of package bax2bam |
Release | Version | Architectures |
VCS | 0.0.9-1 | all |
|
License: BSD-3-clause
Debian package not available
Version: 0.0.9-1
|
The program bax2bam converts the legacy PacBio basecall format (bax.h5) into
the BAM basecall format.
|
biceps
error-tolerant peptide identification
|
Versions of package biceps |
Release | Version | Architectures |
VCS | 0.0.201401-1 | all |
|
License: BSDlike
Debian package not available
Version: 0.0.201401-1
|
BICEPS is tool for the error-tolerant identification of peptides based
on a statistical regularization scheme. It balances possible
improvements in peptide-spectrum-matches by allowing substitutions
against the increased risk of false positives. BICEPS can identify
peptides containing two or more substitutions as occuring e.g. in
cross-species searches.
|
bigsdb
Bacterial Isolate Genome Sequence Database
|
Versions of package bigsdb |
Release | Version | Architectures |
VCS | 1.18.1-1 | all |
|
License: GPL2+
Debian package not available
Version: 1.18.1-1
|
The Bacterial Isolate Genome Sequence Database (BIGSdb) is a scalable,
web-accessible database system designed to store and analyse linked
phenotypic and genotypic information in a computationally efficient
manner. Sequence data can range from single sequence reads to multiple
contigs generated by whole genome sequencing technologies. The system
incorporates the capacity to define and identify any number of loci and
genetic variants at those loci within the stored nucleotide sequences.
These loci can be further organised into schemes for isolate
characterisation or for evolutionary or functional analyses.
|
bismark
bisulfite read mapper and methylation caller
|
Versions of package bismark |
Release | Version | Architectures |
VCS | 0.22.3-1 | all |
|
License: GPL-3+
Debian package not available
Version: 0.22.3-1
|
Bismark is a program to map bisulfite treated sequencing reads to a
genome of interest and perform methylation calls in a single step. The
output can be easily imported into a genome viewer, such as SeqMonk, and
enables a researcher to analyse the methylation levels of their samples
straight away. It's main features are:
- Bisulfite mapping and methylation calling in one single step
- Supports single-end and paired-end read alignments
- Supports ungapped and gapped alignments
- Alignment seed length, number of mismatches etc. are adjustable
- Output discriminates between cytosine methylation in CpG, CHG and
CHH context
|
blat
BLAST-Like Alignment Tool
|
Versions of package blat |
Release | Version | Architectures |
VCS | 35-1 | all |
|
License: FreeForScientificUse
Debian package not available
Version: 35-1
|
BLAT on DNA is designed to quickly find sequences of 95% and greater
similarity of length 25 bases or more. It may miss more divergent or shorter
sequence alignments. It will find perfect sequence matches of 25 bases, and
sometimes find them down to 20 bases. BLAT on proteins finds sequences of 80%
and greater similarity of length 20 amino acids or more. In practice DNA BLAT
works well on primates, and protein blat on land vertebrates.
BLAT is not BLAST. DNA BLAT works by keeping an index of the entire genome in
memory. The index consists of all non-overlapping 11-mers except for those
heavily involved in repeats. The index takes up a bit less than a gigabyte of
RAM. The genome itself is not kept in memory, allowing BLAT to deliver high
performance on a reasonably priced Linux box. The index is used to find areas
of probable homology, which are then loaded into memory for a detailed
alignment. Protein BLAT works in a similar manner, except with 4-mers rather
than 11-mers. The protein index takes a little more than 2 gigabytes.
|
blobology
tool set for the visualisation of genome assemblies
|
Versions of package blobology |
Release | Version | Architectures |
VCS | 0.0+20151216-1 | all |
|
License: MIT
Debian package not available
Version: 0.0+20151216-1
|
Tools for making blobplots or Taxon-Annotated-GC-Coverage plots
(TAGC plots) to visualise the contents of genome assembly data sets
as a QC step.
blobtools consist of a series of tools that can be used to
- collate information associated with an assembly file, such as:
- sequence ID
- sequence length
- GC-content
- coverage information
- taxonomy information (sequence similarity search hits)
- user-defined categories
- visualise information using blobplots, covplots and/or readcovplots.
- extract information into human- and computer-readable files
- produce paper-ready figures
|
braker
annotating protein coding genes in genomes.
|
Versions of package braker |
Release | Version | Architectures |
VCS | 2.1.2+dfsg-1 | all |
|
License: Artistic-1.0
Debian package not available
Version: 2.1.2+dfsg-1
|
Genomic DNA controls the behaviour of biological cells. Understanding it,
and its variations, facilitates the molecular pathology of diseases.
braker.pl can either run with a genome sequence, only; or with additional
alignments for short transcriptome reads against the genome; or with
additional protein sequences of closely related species; or with evidence
from the alignment of protein sequences of distantly related species.
The package provides the means to interpret genomic sequences in FASTA format
from fungi, plants and animals.
|
card-rgi
analysis of genome sequences using the Resistance Gene Identifier
|
Versions of package card-rgi |
Release | Version | Architectures |
VCS | 4.2.2-1 | all |
|
License: non-free
Debian package not available
Version: 4.2.2-1
|
The Comprehensive Antibiotic Resistance Database ("CARD") provides data,
models, and algorithms relating to the molecular basis of antimicrobial
resistance. The CARD provides curated reference sequences and SNPs
organized via the Antibiotic Resistance Ontology ("ARO"). These data can
be browsed on the website or downloaded in a number of formats. These
data are additionally associated with detection models, in the form of
curated homology cut-offs and SNP maps, for prediction of resistome from
molecular sequences. These models can be downloaded or can be used for
analysis of genome sequences using the Resistance Gene Identifier
("RGI"), either online or as a stand-alone tool.
Please cite:
Baofeng Jia, Amogelang R. Raphenya, Brian Alcock, Nicholas Waglechner, Peiyao Guo, Kara K. Tsang, Briony A. Lago, Biren M. Dave, Sheldon Pereira, Arjun N. Sharma, Sachin Doshi, Mélanie Courtot, Raymond Lo, Laura E. Williams, Jonathan G. Frye, Tariq Elsayegh, Daim Sardar, Erin L. Westman, Andrew C. Pawlowski, Timothy A. Johnson, Fiona S.L. Brinkman, Gerard D. Wright and Andrew G. McArthur:
CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database.
(PubMed,eprint)
Nucleic Acids Research
45(D1):D566-D573
(2017)
|
cellprofiler
quantitatively measure phenotypes from images automatically
|
Versions of package cellprofiler |
Release | Version | Architectures |
VCS | 3.0.0-1 | all |
|
License: GPL-2
Debian package not available
Version: 3.0.0-1
|
CellProfiler is cell image analysis software designed to enable
biologists without training in computer vision or programming to
quantitatively measure phenotypes from thousands of images
automatically.
|
cinema
multi-sequence alignment editor and viewer
|
Versions of package cinema |
Release | Version | Architectures |
VCS | 3.0.23-1 | all |
|
License: LGPL
Debian package not available
Version: 3.0.23-1
|
It has been designed to be as extensible as possible. Notes of this
extensibility can be found in "EXTENDING_CINEMA", and the
"cinema-module" sub-directory.
Cinema currently has limited support for various sequence formats,
although its easy to add new ones. A large number of alignments in the
appropriate format can be found as part of the align compendium at
|
condetri
straight-forward trimming of FASTQ sequences
|
Versions of package condetri |
Release | Version | Architectures |
VCS | 2.3-1 | all |
|
License: <license>
Debian package not available
Version: 2.3-1
|
This package is a simplistic contribution to the wealth of tools for
trimming of sequences of current Next-Generation-Sequencing data. It
was developed in the context of de novo whole-genome assembly.
The tool reads from the 3'-end and extract reads (or read pairs) of good
quality. If the reads are paired, the filtering is done pairwise, and
if one read in a pair has low quality, the remaining read is saved as
single end.
|
contrafold
CONditional TRAining for RNA Secondary Structure Prediction
|
Versions of package contrafold |
Release | Version | Architectures |
VCS | 2.02-1 | all |
|
License: BSD-3-Clause
Debian package not available
Version: 2.02-1
|
For several decades, free energy minimization methods have been the dominant
strategy for single sequence RNA secondary structure prediction. More
recently, stochastic context-free grammars (SCFGs) have emerged as an
alternative probabilistic methodology for modeling RNA structure. Unlike
physics-based methods, which rely on thousands of experimentally-measured
thermodynamic parameters, SCFGs use fully-automated statistical learning
algorithms to derive model parameters. Despite this advantage, however,
probabilistic methods have not replaced free energy minimization methods as
the tool of choice for secondarystructure prediction, as the accuracies of
the best current SCFGs have yet to match those of the best physics-based
models.
CONTRAfold is a novel secondary structure prediction method based on
conditional log-linear models (CLLMs), a flexible class of probabilistic
models which generalize upon SCFGs by using discriminative training and
feature-rich scoring. By incorporating most of the features found in
typical thermodynamic models, CONTRAfold achieves the highest single
sequence prediction accuracies to date, outperforming currently available
probabilistic and physics-based techniques. Our result thus closes the gap
between probabilistic and thermodynamic models, demonstrating that
statistical learning procedures provide an effective alternative to
empirical measurement of thermodynamic parameters for RNA secondary
structure prediction.
|
covpipe
pipeline to generate consensus sequences from NGS reads
|
Versions of package covpipe |
Release | Version | Architectures |
VCS | 3.0.6-1 | all |
|
License: GPL-3+
Debian package not available
Version: 3.0.6-1
|
CovPipe is a pipeline to generate consensus sequences from NGS reads
based on a reference sequence. The pipeline is tailored to be used for
SARS-CoV-2 data, but may be used for other viruses.
Genomic variants of your NGS data in comparison to a reference will be
determined. These variants will be included into the reference and form
the consensus sequences. See below for further details on the determined
set of consensus sequences.
|
crossbow
Genotyping from short reads using cloud computing
|
Versions of package crossbow |
Release | Version | Architectures |
VCS | 1.2.0-1 | all |
|
License: Artistic
Debian package not available
Version: 1.2.0-1
|
Crossbow is a scalable software pipeline for whole genome resequencing
analysis. It combines Bowtie, an ultrafast and memory efficient short read
aligner, and SoapSNP, an accurate genotyper, within Hadoop to distribute and
accelerate the computation with many nodes. The pipeline can accurately analyze
over 35x coverage of a human genome in one day on a 10-node local cluster, or
in 3 hours for about $100 using a 40-node, 320-core cluster rented from
Amazon's EC2 utility computing service.
|
crux-toolkit
toolkit for tandem mass spectrometry analysis
|
Versions of package crux-toolkit |
Release | Version | Architectures |
VCS | 3.1-1 | all |
|
License: Apache-2.0
Debian package not available
Version: 3.1-1
|
The Crux mass spectrometry analysis toolkit is an open source project
that aims to provide users with a cross-platform suite of analysis tools
for interpreting protein mass spectrometry data. The toolkit includes
several search engines for both standard and cross-linked database
search, as well as a variety of pre- and post-processing engines for
assigning high-resolution precursor masses to spectra, assigning
statistical confidence estimates to spectra, peptides and proteins, and
performing label free quantification.
Please cite:
Sean McIlwain, Kaipo Tamura, Attila Kertesz-Farkas, Charles E. Grant, Benjamin Diament, Barbara Frewen, J. Jeffry Howbert, Michael R. Hoopmann, Lukas Käll, Jimmy K. Eng, Michael J. MacCoss and William Stafford Noble:
Crux: rapid open source protein tandem mass spectrometry analysis.
(PubMed)
2014
13(10):4488-4491
(Journal of Proteome Research)
|
cytoscape
visualizing molecular interaction networks
|
Versions of package cytoscape |
Release | Version | Architectures |
VCS | 3.1.0-1 | all |
|
License: LGPL-2.1
Debian package not available
Version: 3.1.0-1
|
Cytoscape is an open source bioinformatics software platform for visualizing
molecular interaction networks and biological pathways and integrating these
networks with annotations, gene expression profiles and other state data.
Although Cytoscape was originally designed for biological research, now it is
a general platform for complex network analysis and visualization.
Cytoscape core distribution provides a basic set of features for data
integration and visualization.
|
dazzle
|
Versions of package dazzle |
Release | Version | Architectures |
VCS | 1.01r3643-1 | all |
|
License: LGP-2+
Debian package not available
Version: 1.01r3643-1
|
Dazzle is a general purpose server for the Distributed Annotation System
(DAS) protocol. It is implemented as a Java servlet, using the BioJava
APIs. Dazzle is a modular system which uses small "datasource" plugins to
provide access to a range of databases. Several general-purpose plugins
are included in the package, and it it straightforward to develop new
plugins to connect to your own databases.
Information on DAS is available from http://www.biodas.org/
|
deepbinner
demultiplexing barcoded Oxford Nanopore sequencing reads
|
Versions of package deepbinner |
Release | Version | Architectures |
VCS | 0.2.0-1 | all |
|
License: GPL-3
Debian package not available
Version: 0.2.0-1
|
Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore
sequencing reads. It does this with a deep convolutional neural network
classifier, using many of the architectural advances that have proven
successful in image classification. Unlike other demultiplexers (e.g.
Albacore and Porechop), Deepbinner identifies barcodes from the raw
signal (a.k.a. squiggle) which gives it greater sensitivity and fewer
unclassified reads.
Reasons to use Deepbinner:
- To minimise the number of unclassified reads (use Deepbinner
by itself).
- To minimise the number of misclassified reads (use Deepbinner in
conjunction with Albacore demultiplexing).
- You plan on running signal-level downstream analyses, like
Nanopolish. Deepbinner can demultiplex the fast5 files which makes
this easier. Reasons to not use Deepbinner:
- You only have basecalled reads not the raw fast5 files (which
Deepbinner requires).
- You have a small/slow computer. Deepbinner is more computationally
intensive than Porechop.
- You used a sequencing/barcoding kit other than the ones Deepbinner
was trained on.
|
dendroscope
analyzing and visualizing rooted phylogenetic trees and networks
|
Versions of package dendroscope |
Release | Version | Architectures |
VCS | 3.0+git20190219.a00d9b9+dfsg-1 | all |
|
License: GPL-3+
Debian package not available
Version: 3.0+git20190219.a00d9b9+dfsg-1
|
Dendroscope 3 is a new program for working with rooted phylogenetic
trees and networks. It provides a number of methods for drawing and
comparing rooted phylogenetic networks, and for computing them from
rooted trees. The program can be used interactively or in
command-line mode.
|
diann
data-independent acquisition (DIA) proteomics data processing
|
Versions of package diann |
Release | Version | Architectures |
VCS | 1.8+dfsg-1 | all |
|
License: AS-IS
Debian package not available
Version: 1.8+dfsg-1
|
DIA-NN - a universal software for data-independent acquisition (DIA)
proteomics data processing by Demichev, Ralser and Lilley labs. In 2018,
DIA-NN opened a new chapter in proteomics, introducing a number of
algorithms which enabled reliable, robust and quantitatively accurate
large-scale experiments using high-throughput methods.
|
ecell
Concept and environment for constructing virtual cells on computers
|
Versions of package ecell |
Release | Version | Architectures |
VCS | 3.2.2-1 | all |
|
License: GPL
Debian package not available
Version: 3.2.2-1
|
The E-Cell Project is an international research project aiming at
developing necessary theoretical supports, technologies and software
platforms to allow precise whole cell simulation.
The E-Cell System is an object-oriented software suite for modeling,
simulation, and analysis of large scale complex systems such as
biological cells, architected by Kouichi Takahashi and written by a team
of developers.
The core part of the system, E-Cell Simulation Environment version 3,
allows many components driven by multiple algorithms with different
timescales to coexist.
E-Cell System consists of the following three major parts:
- E-Cell Simulation Environment (or E-Cell SE)
- E-Cell Modeling Environment (or E-Cell ME)
- E-Cell Analysis Toolkit
This package contains all these parts, only the documentation is
distributed separately.
|
ensembl
basic Ensembl genome browser
|
Versions of package ensembl |
Release | Version | Architectures |
VCS | 98+git20190619.e98e194-1 | all |
|
License: free
Version: 98+git20190619.e98e194-1
|
Ensembl is a joint project of the Sanger Center and the European
Bioinformatics Institute, an outstation of the European Molecular
Biology Laboratory, (EMBL-EBI) that are sharing a campus in Hinxton
near Cambridge, UK. It presents the sequence data for the
yet available complete genomes of many vertebrates and is helped
by many sister-projects to cover also plants, invertebrates
and bacteria.
This package provides a basic installation of Ensembl. It comprises
a full copy of the public Ensembl website, minus Blast and SSAHA,
and minus BioMart. It uses UniSearch instead of the engine used on the
public site for searching by keyword. It connects directly to the public
databases hosted by the EBI/Sanger.
This is meant as an easy way to get a basic Ensembl installation
working on Debian. It can then be customised to local requirements.
Note that Ensembl has two odd dependencies: bioperl1.2.3 and
libparallel-useragent-perl. Those are not required for routine
browsing, but the bioperl1.2.3 library performs the parsing of BLAST
outputs. Version 1.2.3 is in conflict with any other existing bioperl
installation and forces you to effectively downgrade.
libwww-perl5.808 will conflict with the latest libwww-perl installation
and thus force a downgrade to 5.808, which will disable many other tools
on your system. Therefore it is advisable NOT to install this package
in parallel with any other software, and/or use a virtual machine or
dedicated machine.
WARNING: Requires internet connection both to install and to run, as it
connects to the Sanger/EBI database servers during both installation
and at runtime.
|
ensembl-vep
Variant Effect Predictor predicting the functional effects of genomic variants
|
Versions of package ensembl-vep |
Release | Version | Architectures |
VCS | 100.2-1 | all |
|
License: Apache-2.0
Debian package not available
Version: 100.2-1
|
The Ensembl Variant Effect Predictor predicts the functional effects of
genomic variants. It has three components:
- VEP (Variant Effect Predictor) predicts the functional effects of
genomic variants.
- Haplosaurus uses phased genotype data to predict whole-transcript
haplotype sequences.
- Variant Recoder translates between different variant encodings.
|
euler-sr
correcting errors in short gene sequence reads and assembling them
|
Versions of package euler-sr |
Release | Version | Architectures |
VCS | 1.1.2-1 | all |
|
License: non_profit
Debian package not available
Version: 1.1.2-1
|
The EULER-SR assembly package contains a suite of programs for
correcting errors in short reads and assembling them. Our assembler may
take as input classical Sanger reads, 454 sequences, and Illumina reads.
|
euler2
de novo repeat classification and fragment assembly
|
Versions of package euler2 |
Release | Version | Architectures |
VCS | 2.0-1 | all |
|
License: free
Debian package not available
Version: 2.0-1
|
Repetitive sequences make up a significant fraction of almost any genome
and an important and still open question in bioinformatics is how to
represent all repeats in DNA sequences. We propose a radically new
approach to repeat classification that is motivated by the fundamental
topological notion of quotient spaces. A torus or Klein bottle are
examples of quotient spaces that can be obtained from a square by gluing
some points. Our new repeat classification algorithm is based on the
observation that the alignment-induced quotient space of a DNA sequence
compactly represents all sequence repeats. This observation leads to a
simple and efficient solution of the repeat classification problem as
well as new approaches to fragment assembly and multiple alignment.
|
exabayes
bayesian phylogenetic tree inference for large-scale analyses
|
Versions of package exabayes |
Release | Version | Architectures |
VCS | 1.5+dfsg-1 | all |
|
License: <license>
Debian package not available
Version: 1.5+dfsg-1
|
ExaBayes is a tool for Bayesian phylogenetic analyses. It implements a
Markov chain Monte Carlo sampling approach that allows to determine the
posterior probability of a tree (resp., topology) and various
evolutionary model parameters, for instance, branch lengths or
substitution rates. Similar approaches are implemented in beast-mcmc or
mrbayes. ExaBayes has heavily drawn inspiration specifically from
the latter one.
ExaBayes comes with the most commonly used evolutionary models, such as
the generalized time reversible model (GTR) of character substitution,
the discretized Gamma-model of among site rate heterogeneity and
estimates trees with unconstrained branch lengths. For clocked tree
models or less parameter-rich substitution models, we refer you to the
established tools.
The distinguishing feature of ExaBayes is its capability to handle
enormous datasets efficiently. ExaBayes provides an implementation of
data parallelism using the Message Passing Interface (MPI). This means,
that if you conduct your analysis on a computing cluster composed of
several machines (a.k.a. nodes), the memory needed to evaluate the
likelihood of trees and parameters given a large alignment can be spread
out across multiple computing nodes. In conclusion, the size of the
concatenated alignment ExaBayes can handle is only limited by the
combined main memory of your entire computing cluster.
|
ffp
Feature Frequency Profile Phylogeny
|
Versions of package ffp |
Release | Version | Architectures |
VCS | 3.19-1 | all |
|
License: non-free
Debian package not available
Version: 3.19-1
|
FFP (Feature frequency profile) is an alignment free comparison tool for
phylogenetic analysis and text comparison. It can be applied to
nucleotide sequences, complete genomes, proteomes and even used for text
comparison.
|
fieldbioinformatics
pipeline with virus identification with Nanopore sequencer
|
Versions of package fieldbioinformatics |
Release | Version | Architectures |
VCS | 1.1.3-1 | all |
|
License: MIT
Debian package not available
Version: 1.1.3-1
|
This is the ARTIC bioinformatics pipeline for working with virus sequencing
data, sequenced with nanopore. It implements a complete bioinformatics
protocol to take the output from the Nanopore sequencer and determine consensus
genome sequences. Includes basecalling, de-multiplexing, mapping, polishing
and consensus generation.
An outbreak of SARS-CoV-2, Ebola, ... something unknown? This
software is field-proven.
|
flappie
flip-flop basecaller for Oxford Nanopore reads
|
Versions of package flappie |
Release | Version | Architectures |
VCS | 2.1.3+ds-1 | all |
|
License: Oxford-Nanopore-PL-1.0
Debian package not available
Version: 2.1.3+ds-1
|
Basecall Fast5 reads using flip-flop basecalling.
Features
|
forester
Graphical vizualiation tool Archaeopteryx
|
Versions of package forester |
Release | Version | Architectures |
VCS | 0.0+20180205-1 | all |
|
License: LGPL 2.1+
Version: 0.0+20180205-1
|
Archaeopteryx is a software tool for the visualization, analysis,
and editing of potentially large and highly annotated phylogenetic trees.
It can be used both as applet (ArchaeopteryxA and ArchaeopteryxE) and
as a standalone application.
|
galaxy
scientific workflow and data integration platform for computational biology
|
Versions of package galaxy |
Release | Version | Architectures |
VCS | 16.10-1 | all |
|
License: TODO
Debian package not available
Version: 16.10-1
|
Galaxy is a scientific workflow, data integration, and data and analysis
persistence and publishing platform that aims to make computational
biology accessible to research scientists that do not have computer
programming or systems administration experience. Although it was
initially developed for genomics research, it is largely domain agnostic
and is now used as a general bioinformatics workflow management system.
|
gatk
The Genome Analysis Toolkit
|
Versions of package gatk |
Release | Version | Architectures |
VCS | 4.2.0.0+dfsg-1 | all |
|
License: Apache-2.0
Debian package not available
Version: 4.2.0.0+dfsg-1
|
The Genome Analysis Toolkit or GATK is a software package developed at
the Broad Institute to analyze high-throughput sequencing data. The
toolkit offers a wide variety of tools, with a primary focus on variant
discovery and genotyping as well as strong emphasis on data quality
assurance. Its robust architecture, powerful processing engine and
high-performance computing features make it capable of taking on
projects of any size.
Please cite:
Aaron McKenna, Matthew Hanna, Eric Banks, Andrey Sivachenko, Kristian Cibulskis, Andrew Kernytsky, Kiran Garimella, David Altshuler, Stacey Gabriel, Mark Daly and Mark A. DePristo:
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data.
(PubMed,eprint)
Genome Research
20(9):1297-303
(2010)
|
gerp++
identifies constrained elements in multiple alignments
|
Versions of package gerp++ |
Release | Version | Architectures |
VCS | 2.1-1 | all |
|
License: GPL-3+
Debian package not available
Version: 2.1-1
|
GERP is a package for analyzing evolutionary rates and finding constrained
elements in a multiple alignment. It uses the notion of "rejected
substitutions" (RS) in order to quantify constraint at individual positions
as well as over elements spanning multiple positions.
GERP consists of two main components: gerpcol, which analyzes multiple
alignments and computes RS scores for all positions, and gerpelem, which
finds constrained elements given the RS scores produced by gerpcol.
|
gramalign
multiple alignment of biological sequences
|
Versions of package gramalign |
Release | Version | Architectures |
VCS | 3.0-1 | all |
|
License: Free-for-adacemia
Debian package not available
Version: 3.0-1
|
GramAlign is a time-efficient progressive Multiple Sequence Alignment
(MSA) algorithm. The novelty of GramAlign comes from the sequence
distance estimation step, whereby distances are determined by the
natural grammar present in nucleotide and amino acid sequences.
|
graphbin
refined binning of metagenomic contigs using assembly graphs
|
Versions of package graphbin |
Release | Version | Architectures |
VCS | 1.1-1 | all |
|
License: GPL-2.0+
Debian package not available
Version: 1.1-1
|
GraphBin is a NGS data-based metagenomic contig bin refinment tool that
makes use of the contig connectivity information from the assembly graph
to bin contigs. It utilizes the binning result of an existing binning
tool and a label propagation algorithm to correct mis-binned contigs and
predict the labels of contigs which are discarded due to short length.
|
graphmap2
highly sensitive and accurate mapper for long, error-prone reads
|
Versions of package graphmap2 |
Release | Version | Architectures |
VCS | 0.6.4-1 | all |
|
License: MIT
Debian package not available
Version: 0.6.4-1
|
GraphMap2 is a highly sensitive and accurate mapper for long, error-
prone reads. The mapping algorithm is designed to analyse nanopore
sequencing reads, which progressively refines candidate alignments to
robustly handle potentially high-error rates and a fast graph traversal
to align long reads with speed and high precision (>95%). Evaluation on
MinION sequencing data sets against short- and long-read mappers
indicates that GraphMap increases mapping sensitivity by 10–80% and maps
95% of bases. GraphMap alignments enabled single-nucleotide variant
calling on the human genome with increased sensitivity (15%) over the
next best mapper, precise detection of structural variants from length
100 bp to 4 kbp, and species and strain-specific identification of
pathogens using MinION reads.
|
haploview
Analysis and visualization of LD and haplotype maps
|
Versions of package haploview |
Release | Version | Architectures |
VCS | 4.1-1 | all |
|
License: MIT
Debian package not available
Version: 4.1-1
|
This tools assists in the analysis of the nucleotide
variation in a population. Such investigations are performed
to determine genes and genetic pathways that are associated
with diseases. This is an early stage in the quest for new drugs.
|
hawkeye
Interactive Visual Analytics Tool for Genome Assemblies
|
Versions of package hawkeye |
Release | Version | Architectures |
VCS | 3.1.0-1 | all |
|
License: Artistic
Debian package not available
Version: 3.1.0-1
|
Genome assembly remains an inexact science. Even when accomplished
with the best software available, the assembly of a genome often
contains numerous errors, both small and large. Hawkeye is a visual
analytics tool for genome assembly analysis and validation, designed
to aid in identifying and correcting assembly errors. Hawkeye blends
the best practices from information and scientific visualization to
facilitate inspection of large-scale assembly data while minimizing
the time needed to detect mis-assemblies and make accurate judgments
of assembly quality.
All levels of the assembly data hierarchy are made accessible to
users, along with summary statistics and common assembly metrics. A
ranking component guides investigation towards likely mis-assemblies
or interesting features to support the task at hand. Wherever
possible, high-level overviews, dynamic filtering, and automated
clustering are leveraged to focus attention and highlight anomalies
in the data. Hawkeyes effectiveness has been proven on several genome
projects, where it has been used both to improve quality and to
validate the correctness of complex genomes.
Hawkeye is compatible with most widely used assemblers, including
Phrap, ARACHNE, Celera Assembler, Newbler, AMOS, and assemblies
deposited in the NCBI Assembly Archive.
|
htqc
Quality control and filtration for illumina sequencing data
|
Versions of package htqc |
Release | Version | Architectures |
VCS | 1.92.3-1 | all |
|
License: GPL-3+
Debian package not available
Version: 1.92.3-1
|
HTQC is a toolkit including statistics tool for illumina high-throughput
sequencing data, and filtration tools for sequence quality, length, tail
quality, etc..
|
idefix
index checking for improved demultiplexing of NGS data
|
Versions of package idefix |
Release | Version | Architectures |
VCS | 1.3-1 | all |
|
License: LGPL-3+
Debian package not available
Version: 1.3-1
|
IDeFIX is a tool for demultiplexing Illumina NGS data.
It reports inconsistencies between the raw data and the Sample Sheet,
checks for duplicates of indices/ index combinations in the latter and
removes unwanted characters from it. Apart from messages printed on the
terminal, IDeFIX creates an IDeFIX_Report.csv containing the indices/
index combinations from the raw data and their abundance as well as
their count in the Sample Sheet and the corresponding Index ID(s). This
file is stored in the project folder.
|
inspect
mass-spectrometry database search tool
|
Versions of package inspect |
Release | Version | Architectures |
VCS | 0.0.20120109-1 | all |
|
License: non-profit
Debian package not available
Version: 0.0.20120109-1
|
Inspect is a MS/MS database search tool specifically designed to address
two crucial needs of the proteomics comminuty: post-translational
modification identification and search speed. The program is available
as a free download or online in the ProteoSAFe webserver. The online
interface is coordinated with other proteomics software developed in the
lab, like PepNovo
Typical database searches do not deal well with the dynamic nature of
the proteome. Post-translational modifications, alternative splicing,
and laboratory chemisty all affect protein behavior and make spectrum
interpretation more challenging. The primary challenge is that the
"virtual database" of all modified peptides undergoes a combinatorial
explosion when a broad range of modifications is allowed. This affects
search running time. A secondary challenge is that in this richer
database, there are many more close "relatives" for each peptide. This
affects scoring accuracy, since differentiating between correct and
incorrect identifications is more difficult.
InsPecT addresses several algorithmic problems in order to identify
modified proteins.
InsPecT uses peptide sequence tags (PSTs) to filter the database.
InsPecT has an internal tag generator, but can accept tags generated by
other tools (e.g. Pepnovo, GutenTAG). Because de novo is imperfect,
multiple tags are produced for each spectrum, to ensure that (at least)
one tag is corrrect. These PSTs are extremely efficient filters, even in
the context of up to a dozen possible modifications. Tag-based filtering
can also be combined with the "two-pass" filtering pioneered by
X!Tandem, where from one search provides a list of proteins (a mini-
database) for a more detailed search.
Unanticipated modifications are common in proteomics. InsPecT implements
the MS-Alignment algorithm for "blind" spectral search, with no bias
toward anticipated modification types. This search has been applied to
annotate heavily-modified proteins such as crystallins.
|
jbrowse
genome browser with an AJAX-based interface
|
Versions of package jbrowse |
Release | Version | Architectures |
VCS | 1.2.3-1 | all |
|
License: GPL-3.0+
Debian package not available
Version: 1.2.3-1
|
JBrowse is a genome browser with an AJAX-based interface. JBrowse renders most
tracks using client side JavaScript and JSON as its data transfer format.
JBrowse is the official successor to GBrowse.
|
kempbasu
significance tests for comparing digital gene expression profiles
|
Versions of package kempbasu |
Release | Version | Architectures |
VCS | 0.9.1-1 | all |
|
License: GPL-3
Debian package not available
Version: 0.9.1-1
|
This package implements the significance tests for comparing digital
gene profiles described in the article:
Varuzza et al. "Significance tests for comparing digital gene
expression profiles"
They provide two programs: kemp for the frequentist test and basu for
the Bayesian test, and some auxiliary scripts.
|
mach-haplotyper
Markov Chain based SNP haplotyper
|
Versions of package mach-haplotyper |
Release | Version | Architectures |
VCS | 1.0.18-1 | all |
|
License: non-free
Debian package not available
Version: 1.0.18-1
|
Recent advancements in chip-based DNA genotyping allow to infer DNA
variants that are not part of the chip but known to be associated
with a combination of SNPs that are measured.
|
mage2tab
MAGE-MLv1 converter and visualiser
|
Versions of package mage2tab |
Release | Version | Architectures |
VCS | 0.9-1 | all |
|
License: CBIL-1.0
Debian package not available
Version: 0.9-1
|
This tool-kit is part of MR_T, a framework for import or export various of
MAGE (MicroArray Gene Expression) documents (MAGE-MLv1, MAGE-TAB, SOFT,
MINiML) from or into databases like GUS (the Genomics Unified Schema,
www.gusdb.org).
This package provides the following programs:
mage2tab — MAGE-MLv1 to MAGE-TAB converter
mage2graph — GraphViz-based mage data visualisation tool
mage-checker — Validation tool
|
manta
structural variant and indel caller for mapped sequencing data
|
Versions of package manta |
Release | Version | Architectures |
VCS | 1.6.0+dfsg-1 | all |
|
License: GPL-3+
Debian package not available
Version: 1.6.0+dfsg-1
|
Manta calls structural variants (SVs) and indels from mapped paired-end
sequencing reads. It is optimized for analysis of germline variation in
small sets of individuals and somatic variation in tumor/normal sample
pairs. Manta discovers, assembles and scores large-scale SVs, medium-
sized indels and large insertions within a single efficient workflow.
The method is designed for rapid analysis on standard compute hardware:
NA12878 at 50x genomic coverage is analyzed in less than 20 minutes on a
20 core server, and most WGS tumor/normal analyses can be completed
within 2 hours. Manta combines paired and split-read evidence during SV
discovery and scoring to improve accuracy, but does not require split-
reads or successful breakpoint assemblies to report a variant in cases
where there is strong evidence otherwise. It provides scoring models for
germline variants in small sets of diploid samples and somatic variants
in matched tumor/normal sample pairs. There is experimental support for
analysis of unmatched tumor samples as well. Manta accepts input read
mappings from BAM or CRAM files and reports all SV and indel inferences
in VCF 4.1 format.
|
marginphase
simultaneous haplotyping and genotyping
|
Versions of package marginphase |
Release | Version | Architectures |
VCS | 0.0+git20181109.cdf139e-1 | all |
|
License: Expat
Debian package not available
Version: 0.0+git20181109.cdf139e-1
|
MarginPhase is a program for simultaneous haplotyping and genotyping.
It is an experimental, open source implementation written in C and
developed to work primarily with nanopore data. The MarginPhase workflow
includes an alignment summation step. This differentiates it from WhatsHap,
which performs a local realignment around analyzed sites. MarginPhase can
also phase genotypic variants simultaneously after filtering out the sites
that are likely homozygous. MarginPhase’s output includes a BAM which
encodes the phasing of each read, including which phase set it is in,
which haplotype it belongs to, and what of the aligned portion falls
into each phase set. Reads which span a phase set boundary have information
for both encoded in them.
|
martj
distributed data integration system for biological data
|
Versions of package martj |
Release | Version | Architectures |
VCS | 0.9+dfsg-1 | all |
|
License: LGPL-2+
Debian package not available
Version: 0.9+dfsg-1
|
BioMart is a simple, distributed data integration system with powerful
query capabilities. The BioMart data model has been applied
to the following data sources: UniProt Proteomes, Macromolecular
Structure Database (MSD), Ensembl, Vega, and dbSNP.
It has been designed to provide researchers with an easy and interactive
access to both the wealth of data available on the Internet and for
in house data integration. BioMart is a successor to the generic
query system originally developed for the Ensembl genome database
(EnsMart). Building on its success, BioMart, has now been applied to
other biological databases.
|
medaka
sequence correction provided by ONT Research
|
Versions of package medaka |
Release | Version | Architectures |
VCS | 1.0.3+dfsg-1 | all |
|
License: MPL-2.0
Debian package not available
Version: 1.0.3+dfsg-1
|
Medaka is a tool to create a consensus sequence from nanopore sequencing
data. This task is performed using neural networks applied from a pileup
of individual sequencing reads against a draft assembly. It outperforms
graph-based methods operating on basecalled data, and can be competitive
with state-of-the-art signal-based methods, whilst being much faster.
Features
- Requires only basecalled data. (.fasta or .fastq)
- Improved accurary over graph-based methods (e.g. Racon).
- 50X faster than Nanopolish (and can run on GPUs).
- Methylation aggregation from Guppy .fast5 files.
- Benchmarks are provided here.
- Includes extras for implementing and training bespoke
correction networks.
|
meme
search for common motifs in DNA or protein sequences
|
Versions of package meme |
Release | Version | Architectures |
VCS | 5.5.5-1 | all |
|
License: non-free
Debian package not available
Version: 5.5.5-1
|
MEME (Multiple EM for Motif Elicitation) is a tool for discovering
motifs in a group of related DNA or protein sequences. A motif is a
sequence pattern that occurs repeatedly in a group of related protein or
DNA sequences. MEME represents motifs as position-dependent
letter-probability matrices which describe the probability of each
possible letter at each position in the pattern. Individual MEME motifs
do not contain gaps. Patterns with variable-length gaps are split by
MEME into two or more separate motifs.
MEME takes as input a group of DNA or protein sequences (the training set)
and outputs as many motifs as requested. MEME uses statistical modeling
techniques to automatically choose the best width, number of occurrences,
and description for each motif.
|
mesquite
modular system for evolutionary analysis
|
Versions of package mesquite |
Release | Version | Architectures |
VCS | 3.04+dfsg.1-1 | all |
|
License: <license>
Debian package not available
Version: 3.04+dfsg.1-1
|
Mesquite is modular, extendible software for evolutionary biology,
designed to help biologists organize and analyze comparative data about
organisms. Its emphasis is on phylogenetic analysis, but some of its
modules concern population genetics, while others do non-phylogenetic
multivariate analysis. Because it is modular, the analyses available
depend on the modules installed.
Mesquite also has many features for managing and processing data,
including processing of chromatograms, sequence alignment, editing of
morphometric data, and others.
|
metabit
analysing microbial profiles from high-throughput sequencing shotgun data
|
Versions of package metabit |
Release | Version | Architectures |
VCS | 0.0+git20170725.24cb3ee+dfsg-1 | all |
|
License: expat
Debian package not available
Version: 0.0+git20170725.24cb3ee+dfsg-1
|
MetaBIT is an integrative and automated metagenomic pipeline for
analysing microbial profiles from high-throughput sequencing
shotgun data.
The metaBIT pipeline proposes tools for visualising microbial profiles
(barplots, heatmaps) and performing a range of statistical analyses
(diversity indices, hierarchical clustering and principal coordinate
analysis). It uses as input fastq files containing trimmed reads from
shotgun high through-put sequencing.
|
modeller
Protein structure modeling by satisfaction of spatial restraints
|
Versions of package modeller |
Release | Version | Architectures |
VCS | 9.19-1 | all |
|
License: non-free_academic
Version: 9.19-1
|
MODELLER is used for homology or comparative modeling of protein
three-dimensional structures (1). The user provides an alignment of a
sequence to be modeled with known related structures and MODELLER automatically
calculates a model containing all non-hydrogen atoms. MODELLER implements
comparative protein structure modeling by satisfaction of spatial restraints
(2, 3), and can perform many additional tasks, including de novo modeling of
loops in protein structures, optimization of various models of protein
structure with respect to a flexibly defined objective function, multiple
alignment of protein sequences and/or structures, clustering, searching of
sequence databases, comparison of protein structures, etc.
|
molekel
Advanced Interactive 3D-Graphics for Molecular Sciences
|
Versions of package molekel |
Release | Version | Architectures |
VCS | 5.4-1 | all |
|
License: free
Debian package not available
Version: 5.4-1
|
Molekel is an open-source multi-platform molecular visualization program.
Some of the features are:
- Different methods to speed-up rendering of molecules with support
for billboards and view-dependent level of detail techniques
- Programmable shaders; standard shaders to enhance rendering quality,
outline contours and perform sketch-like renderings are provided
- Visualization of residues (ribbon or schematic)
- Complete control over the generation of molecular surfaces (bounding
box and resolution)
- Visualization of the following surfaces:
- Orbitals
- Iso-surface from density matrix
- Iso-surface from Gaussian cube grid data
- SAS
- SES
- Van der Waals
- Animation of molecular surfaces
- Animation of vibrational modes
- Export high resolution images for 300+ DPI printing
- Export to PostScript and PDF
- Export animation
- Plane widget to visualize a scalar field: the plane can be freely
moved in 3d space and the points on the plane surface will be colored
according to the value of the scalar field: a cursor can be moved on
the plane surface to show the exact value of the field at a specific
point in space.
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mosaik-aligner
reference-guided aligner for next-generation sequencing
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Versions of package mosaik-aligner |
Release | Version | Architectures |
VCS | 2.2.30+20140627-1 | all |
|
License: MIT
Debian package not available
Version: 2.2.30+20140627-1
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MosaikBuild converts various sequence formats into Mosaik’s native read
format. MosaikAligner pairwise aligns each read to a specified series of
reference sequences. MosaikSort resolves paired-end reads and sorts the
alignments by the reference sequence coordinates. Finally, MosaikText
converts alignments to different text-based formats.
At this time, the workflow consists of supplying sequences in FASTA,
FASTQ, Illumina Bustard & Gerald, or SRF file formats and producing
results in the BLAT axt, the BAM/SAM, the UCSC Genome Browser bed, or
the Illumina ELAND formats.
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mpsqed
alignment editor and multiplex pyrosequencing assay designer
|
Versions of package mpsqed |
Release | Version | Architectures |
VCS | 0.9.3-1 | all |
|
License: LGPL-2+
Debian package not available
Version: 0.9.3-1
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Molecular-based diagnostic assays are the gold standard for infectious
diseases today, since they allow a rapid and sensitive identification
and typing of various pathogens. While PCR can be designed to be
specific for a certain pathogen, a subsequent sequence analysis is
frequently required for confirmation or typing. The design of
appropriate PCR-based assays is a complex task, especially when
conserved discriminating polymorphisms are rare or if the number of
types which need to be differentiated is high. One extremely useful but
underused method for this purpose is the multiplex pyrosequencing
technique. mPSQed is a program developed at the Robert Koch Institute
and targeted at facilitating the creation of such assays.
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mugsy
multiple whole genome alignment tool
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Versions of package mugsy |
Release | Version | Architectures |
VCS | 1r2.3+dfsg-1 | all |
|
License: Artistic-2.0
Debian package not available
Version: 1r2.3+dfsg-1
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Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for
pairwise alignment, a custom graph based segmentation procedure for
identifying collinear regions, and the segment-based progressive
multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft
genomes in the form of multi-FASTA files and does not require a
reference genome.
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mview
biological sequence alignment conversion
|
Versions of package mview |
Release | Version | Architectures |
VCS | 1.67+dfsg1-1 | all |
|
License: GPL-2.0+
Debian package not available
Version: 1.67+dfsg1-1
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mview is a command line utility that extracts and reformats the results
of a sequence database search or a multiple alignment, optionally adding
HTML markup for web page layout. It can also be used as a filter to
extract and convert searches or alignments to common formats.
Inputs:
- Sequence database search: BLAST, FASTA suites.
-
Multiple sequence alignment: CLUSTAL, HSSP, MSF, FASTA, PIR, MAF
Outputs:
-
HTML, FASTA, CLUSTAL, MSF, PIR, RDB (tab-separated).
The redundancy of that source tree with existing JS packages needs to
be evaluated. In the interim, the package shall remain in experimental.
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nano-snakemake
detection of structural variants in genome sequencing data
|
Versions of package nano-snakemake |
Release | Version | Architectures |
VCS | 1.0+git20200224.ff11b35-1 | all |
|
License: Expat
Debian package not available
Version: 1.0+git20200224.ff11b35-1
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To "have a genetic variation" may mean many different things. Technically
most straight forward to investigate are changes to single positions in
the long DNA chains - every chromosome is a single polymer of nucleic acids.
This is also what we have most data from for many diseases.
But sometimes, DNA that looks completely the same when looking at short reads
at the time (and not feeling lucky), the position looked at may be inverted
on the chromosome. Or it may be a copy of the original site and not a "real"
single-nucleotide polymorphism (SNP). Or it may have translocated to
another chromosome.
These are examples for structural changes to the DNA. Individuals may never
notice them. Or there may be a higher chances to develop a disease or it may
affect fertility. Technologies like the Nanopore have emerged that can read
longer segments of the DNA, so one can see multiple copies of the same gene
in the same read or at least can assemble the DNA fragments read in a way to
then align the reads non-ambiguously and support the analysis of such
copy-number variations (CNVs).
This snakemake pipeline on nanopore whole genome sequencing data provides
a complete structural variant analysis. Steps implemented and tools
wrapped comprise:
- fast: minimap2 alignment with Sniffles and SVIM SV calling
- precise: ngmlr alignment with Sniffles SV calling
- minimap2: minimap2 alignment with Sniffles, SVIM, NanoSV and npInv SV calling
- minimap2_pbsv: minimap2 alignment with pbsv-specific parameters with
pbsv, SVIM, NanoSV and npInv SV calling
- ngmlr: ngmlr with Sniffles, NanoSV, SVIM and npInv SV calling
- last-prepare: create a LAST index and train aligner parameters using last-train
- last: LAST alignment with tandem-genotypes STR calling
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nanocall
Basecaller for Oxford Nanopore Sequencing Data
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Versions of package nanocall |
Release | Version | Architectures |
VCS | 0.7.4-1 | all |
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License: expat
Debian package not available
Version: 0.7.4-1
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The highly portable Oxford Nanopore MinION sequencer has enabled new
applications of genome sequencing directly in the field. However, the
MinION currently relies on a cloud computing platform, Metrichor
(metrichor.com), for translating locally generated sequencing data into
basecalls.
Nanocall allows offline and private analysis of MinION data. Nanocall is
the first freely-available, open-source basecaller for Oxford Nanopore
sequencing data and does not require an internet connection. Using R7.3
chemistry, on two E.coli and two human samples, with natural as well as
PCR-amplified DNA, Nanocall reads have ~68% identity, directly
comparable to Metrichor "1D" data. Further, Nanocall is efficient,
processing ~2500Kbp of sequence per core hour using the fastest
settings, and fully parallelized. Using a 4 core desktop computer,
Nanocall could basecall a MinION sequencing run in real time. Metrichor
provides the ability to integrate the "1D" sequencing of template and
complement strands of a single DNA molecule, and create a "2D" read.
Nanocall does not currently integrate this technology, and addition of
this capability will be an important future development. In summary,
Nanocall is the first open-source, freely available, off-line basecaller
for Oxford Nanopore sequencing data.
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nanocomp
compare multiple runs of long biological sequences
|
Versions of package nanocomp |
Release | Version | Architectures |
VCS | 1.12.0-1 | all |
|
License: GPL-3.0+
Debian package not available
Version: 1.12.0-1
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NanoClmp compares multiple runs of long read sequencing data and
alignments. It creates violin plots or box plots of length, quality and
percent identity and creates dynamic, overlaying read length histograms
and a cumulative yield plot.
This package installs the 'NanoCalc' executable.
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nanoplot
plotting scripts for long read sequencing data
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Versions of package nanoplot |
Release | Version | Architectures |
VCS | 1.36.2-1 | all |
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License: MIT
Debian package not available
Version: 1.36.2-1
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NanoPlot provides plotting scripts for long read sequencing data.
These scripts perform data extraction from Oxford Nanopore sequencing data
in the following formats:
- fastq files (optionally compressed)
- fastq files generated by albacore, guppy or MinKNOW containing additional
information (optionally compressed)
- sorted bam files
- sequencing_summary.txt output table generated by albacore, guppy or
MinKnow basecalling (optionally compressed)
- fasta files (optionally compressed)
- multiple files of the same type can be offered simultaneously
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ncbi-magicblast
|
Versions of package ncbi-magicblast |
Release | Version | Architectures |
VCS | 1.5.0+ds-1 | all |
|
License: PD
Debian package not available
Version: 1.5.0+ds-1
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Magic-BLAST is a tool for mapping large next-generation RNA or DNA
sequencing runs against a whole genome or transcriptome. Each alignment
optimizes a composite score, taking into account simultaneously the two
reads of a pair, and in case of RNA-seq, locating the candidate introns
and adding up the score of all exons. This is very different from other
versions of BLAST, where each exon is scored as a separate hit and read-
pairing is ignored.
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nextsv
automated structural variation detection for long-read sequencing
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Versions of package nextsv |
Release | Version | Architectures |
VCS | 0.4.0-1 | all |
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License: GB-nonfree
Debian package not available
Version: 0.4.0-1
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NextSV is an computational pipeline that allows structural variant (SV)
calling from PacBio sequencing data using PBhoney and Sniffles. NextSV takes
FASTA or FASTQ files as input. Once the SV caller is selected by user, NextSV
automatically chooses the compatible aligner and performs mapping. The
alignments will be automatically sorted and then presented to the SV caller.
Users can change the parameters by modifying its configuration file. When the
analysis is finished, NextSV will examine the FASTA/FASTQ, BAM, and result
files and generate a report showing various statistics. If more than both
callers are selected, NextSV will format the raw result files (.tails, .spots,
or .vcf files) into bed files and generate the intersection or union call set
for the purpose of higher accuracy or sensitivity.
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ngila
global pairwise alignments with logarithmic and affine gap costs
|
Versions of package ngila |
Release | Version | Architectures |
VCS | 1.3-1 | all |
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License: GPLv3
Debian package not available
Version: 1.3-1
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Ngila is an application that will find the best alignment of a pair
of sequences using log-affine gap costs, which are the most
biologically realistic gap costs.
Ngila implements the Miller and Myers (1988) algorithm in order to
find a least costly global alignment of two sequences given homology
costs and a gap cost. Two versions of the algorithm are
included: holistic and divide-and-conquer. The former is faster but
the latter utilizes less memory. Ngila starts with the
divide-and-conquer method but switches to the holistic method for
subsequences smaller than a user-established threshold. This improves
its speed without substantially increasing memory requirements. Ngila
also allows users to assign costs to end gaps that are smaller than
costs for internal gaps. This is important for aligning using the
free-end-gap method.
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ngsqctoolkit
toolkit for the quality control of next generation sequencing data
|
Versions of package ngsqctoolkit |
Release | Version | Architectures |
VCS | 2.3.3-1 | all |
|
License: to_be_clarified
Debian package not available
Version: 2.3.3-1
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NGS QC Toolkit: A toolkit for the quality control (QC) of next
generation sequencing (NGS) data. The toolkit comprises of user-friendly
stand alone tools for quality control of the sequence data generated
using Illumina and Roche 454 platforms with detailed results in the form
of tables and graphs, and filtering of high-quality sequence data. It
also includes few other tools, which are helpful in NGS data quality
control and analysis.
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nw-align
global protein sequence alignment
|
Versions of package nw-align |
Release | Version | Architectures |
VCS | 0.20100803-1 | all |
|
License: free
Debian package not available
Version: 0.20100803-1
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NWalign is simple and robust alignment program for protein
sequence-to-sequence alignments based on the standard Needleman-Wunsch
dynamic programming algorithm. The implementation is performed in
FORTRAN.
This program was tested at 2014-02-01 by Daniel Barker at the Debian
Med sprint and was not functional according to his test.
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oases
de novo transcriptome assembler for very short reads
|
Versions of package oases |
Release | Version | Architectures |
VCS | 0.2.09-1 | all |
|
License: GPL-3
Debian package not available
Version: 0.2.09-1
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Oases is a de novo transcriptome assembler designed to produce
transcripts from short read sequencing technologies, such as Illumina,
SOLiD, or 454 in the absence of any genomic assembly. Oases uploads a
preliminary assembly produced by Velvet, and clusters the contigs into
small groups, called loci. It then exploits the paired-end read and long
read information, when available, to construct transcript isoforms.
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omegamap
describing selection and recombination in sequences
|
Versions of package omegamap |
Release | Version | Architectures |
VCS | 0.5-1 | all |
|
License: GPL-3
Debian package not available
Version: 0.5-1
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OmegaMap is a program for detecting natural selection and recombination
in DNA or RNA sequences. It is based on a model of population
genetics and molecular evolution. The signature of natural selection
is determined by the relative excess of non-synonymous to synonymous
polymorphisms. The signature of recombination is detected from the
patterns of linkage disequilibrium.
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oncofuse
predicting oncogenic potential of gene fusions
|
Versions of package oncofuse |
Release | Version | Architectures |
VCS | 1.1.1-1 | all |
|
License: Apache-2.0
Debian package not available
Version: 1.1.1-1
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Oncofuse is a framework designed to estimate the oncogenic potential of
de-novo discovered gene fusions. It uses several hallmark features and
employs a bayesian classifier to provide the probability of a given gene
fusion being a driver mutation.
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optitype
precision HLA typing from next-generation sequencing data
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Versions of package optitype |
Release | Version | Architectures |
VCS | 1.3.2-1 | all |
|
License: <license>
Debian package not available
Version: 1.3.2-1
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OptiType is a novel HLA genotyping algorithm based on integer linear
programming, capable of producing accurate 4-digit HLA genotyping
predictions from NGS data by simultaneously selecting all major and
minor HLA Class I alleles.
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paipline
Pipeline for the Automatic Identification of Pathogens
|
Versions of package paipline |
Release | Version | Architectures |
VCS | 0.0+git20180416.062bce7-1 | all |
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License: GPL_3+
Debian package not available
Version: 0.0+git20180416.062bce7-1
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This program is designed to search for pathogen nucleic acid sequences
in NGS datasets. It needs databases in the format provided by the database-
updater found under https://gitlab.com/andreas.andrusch/database-updater.
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pangolin
Phylogenetic Assignment of Named Global Outbreak LINeages
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Versions of package pangolin |
Release | Version | Architectures |
VCS | 4.3.1-1 | all |
|
License: GPL-3+
Debian package not available
Version: 4.3.1-1
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Pangolin runs a multinomial logistic regression model trained against
lineage assignments based on GISAID data.
Legacy pangolin runs using a guide tree and alignment hosted at
cov-lineages/lineages. Some of this data is sourced from GISAID, but
anonymised and encrypted to fit with guidelines. Appropriate permissions
have been given and acknowledgements for the teams that have worked to
provide the original SARS-CoV-2 genome sequences to GISAID are also
hosted here.
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partitionfinder
choses partitioning schemes and models of molecular evolution for sequence data
|
Versions of package partitionfinder |
Release | Version | Architectures |
VCS | 2.1.1+dfsg-1 | all |
|
License: GPL-3+
Debian package not available
Version: 2.1.1+dfsg-1
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PartitionFinder and PartitionFinderProtein are Python programs for
simultaneously choosing partitioning schemes and models of molecular evolution
for sequence data. You can use them before running a phylogenetic analysis,
in order to decide how to divide up your sequence data into separate blocks
before analysis, and to simultaneously perform model selection on each of
those blocks.
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patristic
Calculate patristic distances and comparing the components of genetic change
|
Versions of package patristic |
Release | Version | Architectures |
VCS | 0.0.20100817-2 | all |
|
License: free
Debian package not available
Version: 0.0.20100817-2
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Patristic overcomes some logistic barriers to analysing signals in
sequences. In additional to calculating patristic distances, it provides
plots for any combination of matrices, calculates commonly used
statistics, allows data such as isolation dates to be entered and
reorders matrices with matching species or gene labels. It will be used
to analyse rates of mutation and substitutional saturation and the
evolution of viruses.
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pcma
fast and accurate multiple sequence alignment based on profile consistency
|
Versions of package pcma |
Release | Version | Architectures |
VCS | 2.0+20040626-1 | all |
|
License: non-free for commercial
Debian package not available
Version: 2.0+20040626-1
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PCMA (profile consistency multiple sequence alignment) is a progressive
multiple sequence alignment program that combines two different
alignment strategies. Highly similar sequences are aligned in a fast way
as in ClustalW, forming pre-aligned groups. The T-Coffee strategy is
applied to align the relatively divergent groups based on
profile–profile comparison and consistency. The scoring function for
local alignments of pre-aligned groups is based on a novel
profile–profile comparison method that is a generalization of the
PSI-BLAST approach to profile–sequence comparison. PCMA balances speed
and accuracy in a flexible way and is suitable for aligning large
numbers of sequences.
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phylophlan
microbial Tree of Life using 400 universal proteins
|
Versions of package phylophlan |
Release | Version | Architectures |
VCS | 1.1.0-1 | all |
|
License: expat
Debian package not available
Version: 1.1.0-1
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PhyloPhlAn is a computational pipeline for reconstructing highly
accurate and resolved phylogenetic trees based on whole-genome sequence
information. The pipeline is scalable to thousands of genomes and uses
the most conserved 400 proteins for extracting the phylogenetic signal.
PhyloPhlAn also implements taxonomic curation, estimation, and insertion
operations.
The main features of PhyloPhlAn are:
- completely automatic, as the user needs only to provide the
(unannotated) protein sequences of the input genomes (as multifasta
files of peptides - not nucleotides)
- very high topological accuracy and resolution because of the use of
up to 400 previously identified most conserved proteins
- the possibility of integrating new genomes in the already
reconstructed most comprehensive tree of life (3,171 microbial
genomes)
- taxonomy estimation for the newly inserted genomes
- taxonomic curation for the produced phylogenetic trees
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phyloviz-core
phylogenetic inference and data visualization for sequence based typing methods
|
Versions of package phyloviz-core |
Release | Version | Architectures |
VCS | 0.0.20111121-1 | all |
|
License: GPL-3
Debian package not available
Version: 0.0.20111121-1
|
Phyloviz allows the analysis of sequence-based typing methods that
generate allelic profiles and their associated epidemiological data.
For representing the possible evolutionary relationships between
strains identified by allelic profiles it uses the goeBURST algorithm, a
refinement of eBURST algorithm proposed by Feil et al., and its
expansion to generate a complete minimum spanning tree (MST).
Phyloviz is being developed in a modular way to allow its expansion
with novel data analysis algorithms and new visualization modules.
Capabilities
- Modularity allows the creation of plugins to analyse different types of data
- Allows the visualization of data overlaid onto goeBURST and MST results
- Confidence assessment of each link in the graph
- Query the data and see the query results directly onto the graphs
- Search your data set using regular expressions to select what to display
- Export the results as images in various formats: eps, png, gif, pdf, etc
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pigx-scrnaseq
pipeline for checkpointed and distributed scRNA-seq analyses
|
Versions of package pigx-scrnaseq |
Release | Version | Architectures |
VCS | 1.1.7+ds-1 | all |
|
License: <special license>
Debian package not available
Version: 1.1.7+ds-1
|
This package provides a automated workflow for the automated analysis of
single-cell RNA-seq experiments. A series of well-accecpted tools are
connected in Python scripts and controlled via snakemake. This supports
the parallel execution of these workflows and provides checkpointing,
such that interrupted workflows can take up their work again.
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pipasic
Protein Abundance Correction in Metaproteomic Data
|
Versions of package pipasic |
Release | Version | Architectures |
VCS | 0.0.r15-1 | all |
|
License: BSD-3-clause
Debian package not available
Version: 0.0.r15-1
|
Metaproteomic analysis allows studying the interplay of organisms or
functional groups and has become increasingly popular also for
diagnostic purposes. However, difficulties arise due to the high
sequence similarity between related organisms. Further, the state of
conservation of proteins between species can be correlated with their
expression level which can lead to significant bias in results and
interpretation. These challenges are similar but not identical to the
challenges arising in the analysis of metagenomic samples and require
specific solutions.
pipasic (peptide intensity-weighted proteome abundance similarity
correction) is a tool which corrects identification and spectral
counting based quantification results using peptide similarity
estimation and expression level weighting within a non-negative lasso
framework. pipasic has distinct advantages over approaches only
regarding unique peptides or aggregating results to the lowest common
ancestor.
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plato
Analysis, translation, and organization of large-scale genetic data
|
Versions of package plato |
Release | Version | Architectures |
VCS | 2.0.0-1 | all |
|
License: GPL-2+
Debian package not available
Version: 2.0.0-1
|
PLATO is an acronym for "PLatform for the Analysis, Translation,
and Organization of large-scale data". Recent technological advances
enable the study of hundreds of thousands of human single-nucleotide
polymorphisms at the population level. Because strategies for analyzing
these data have not kept pace with the laboratory methods that generate
the data, it is unlikely that these advances will immediately lead to
an improved understanding of the genetic contribution to common human
disease and drug response. Currently, no single analytical method
allows us to extract all available information from a whole-genome
association study. In fact, no single method can be optimal for all
datasets, especially when the genetic architecture for diseases can
vary substantially, as is certainly the case. Therefore, an integrative
platform is needed to accommodate multiple analytical methods for
analysis as we learn more about genetic architecture. As a result,
we are developing a system for the analysis of genome-wide association
data that will incorporate several analytical approaches as filters to
allow a scientist to choose whatever analytical methods they wish to
apply. PLATO (PLatform for the Analysis, Translation, and Organization
of large-scale data) will incorporate a number of filters to select
the important SNPs in a genome-wide association study.
Whole-genome Association Study Pipeline (WASP) has recently been
absorbed into PLATO. WASP was designed to aid in retrieving, evaluating,
formatting, and analyzing genotypic and clinical data from the latest
large-scale genotyping studies. WASP implements a battery of quality
control procedures to assess the data. Among the currently available
procedures are the examination of marker and sample genotyping
efficiency, allele frequency calculations, checks of Mendelian error
(if applicable) and gender discrepancies (based on available chromosome X
and Y genotypes), and tests of Hardy-Weinberg Equilibrium. Additionally,
WASP can retrieve and format data for other software programs such as the
Graphical Representation of Relationships (GRR) program, or STRUCTURE,
and depending on the nature of the samples and the depth of examination
the user desires to pursue. Beyond the quality control aspect of this
application, WASP can perform standard tests of association using the
Transmission Disequilibrium Test TDT for family-based datasets and the
chi-square test of association for case-control datasets.
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pomoxis
analysis components from Oxford Nanopore Research
|
Versions of package pomoxis |
Release | Version | Architectures |
VCS | 0.3.4-1 | all |
|
License: MPL-2.0
Debian package not available
Version: 0.3.4-1
|
Pomoxis comprises a set of basic bioinformatic tools tailored to
nanopore sequencing. Notably tools are included for generating and
analysing draft assemblies. Many of these tools are used by the research
data analysis group at Oxford Nanopore Technologies.
Features
- Wraps third party tools with known good default parameters and
methods of use.
- Creates an isolated environment with all third-party tools.
- Streamlines common short analysis chains.
- Integrates into katuali for performing more complex analysis
pipelines.
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Protein structure alignment
|
Versions of package profit |
Release | Version | Architectures |
VCS | 3.1-1 | all |
|
License: non-distributable
Debian package not available
Version: 3.1-1
|
ProFit is designed to be the ultimate protein least squares fitting
program. It has many features including flexible specification of
fitting zones and atoms, calculation of RMS over different zones or
atoms, RMS-by-residue calculation, on-line help facility, etc.
A symbolic link is provided to have the binary name back to how
it is historically correct.
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psipred
protein secondary structure prediction
|
Versions of package psipred |
Release | Version | Architectures |
VCS | 4.01-1 | all |
|
License: custom
Debian package not available
Version: 4.01-1
|
PSIPRED is a simple and accurate secondary structure prediction
method, incorporating two feed-forward neural networks which perform an
analysis on output obtained from PSI-BLAST (Position Specific Iterated -
BLAST). Using a very stringent cross validation method to evaluate the
method's performance, PSIPRED 2.6 achieves an average Q3 score of 80.7%.
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pssh2
set of scripts for mapping protein sequence to structure
|
Versions of package pssh2 |
Release | Version | Architectures |
VCS | 0.6 | all |
|
License: GPL-2+
Debian package not available
Version: 0.6
|
pssh2 creates sequence-to-structure alignments based on
hhblits profiles built for the query sequence.
pssh2 consists of scripts to run the hhblits queries
and parse the output.
You also need the pdb_full database downloaded from rostlab.org:
ftp://rostlab.org/pssh2/pdb_full/
This package provides the script files needed to run within
PredictProtein.
They are all called in the correct order in pp_pssh2.
It also contains scripts to run independent of PredictProtein.
It assumes you have a mysql database to store information.
The configuration information is kept in pssh2.conf
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pufferfish
Efficient index for the colored, compacted, de Bruijn graph
|
Versions of package pufferfish |
Release | Version | Architectures |
VCS | 1.8.0+dfsg-1 | all |
|
License: GPL-3+
Debian package not available
Version: 1.8.0+dfsg-1
|
Pufferfish is a new time and memory-efficient data structure for indexing a
compacted, colored de Bruijn graph (ccdBG).
Though the de Bruijn Graph (dBG) has enjoyed tremendous popularity as an
assembly and sequence comparison data structure, it has only relatively
recently begun to see use as an index of the reference sequences (e.g. deBGA,
kallisto). Particularly, these tools index the compacted dBG (cdBG), in which
all non-branching paths are collapsed into individual nodes and labeled with
the string they spell out. This data structure is particularly well-suited for
representing repetitive reference sequences, since a single contig in the cdBG
represents all occurrences of the repeated sequence. The original positions in
the reference can be recovered with the help of an auxiliary "contig table"
that maps each contig to the reference sequence, position, and orientation
where it appears as a substring. The deBGA paper has a nice description how
this kind of index looks (they call it a unipath index, because the contigs we
index are unitigs in the cdBG), and how all the pieces fit together to be able
to resolve the queries we care about. Moreover, the cdBG can be built on
multiple reference sequences (transcripts, chromosomes, genomes), where each
reference is given a distinct color (or colour, if you're of the British
persuasion). The resulting structure, which also encodes the relationships
between the cdBGs of the underlying reference sequences, is called the
compacted, colored de Bruijn graph (ccdBG). This is not, of course, the only
variant of the dBG that has proven useful from an indexing perspective. The
(pruned) dBG has also proven useful as a graph upon which to build a path
index of arbitrary variation / sequence graphs, which has enabled very
interesting and clever indexing schemes like that adopted in GCSA2. Also,
thinking about sequence search in terms of the dBG has led to interesting
representations for variation-aware sequence search backed by indexes like the
vBWT (implemented in the excellent gramtools package).
|
purple
Picking Unique Relevant Peptides for viraL Experiments
|
Versions of package purple |
Release | Version | Architectures |
VCS | 0.4.1-1 | all |
|
License: LGPL-3+
Debian package not available
Version: 0.4.1-1
|
Emerging virus diseases present a global threat to public health. To
detect viral pathogens in time-critical scenarios, accurate and fast
diagnostic assays are required. Such assays can now be established using
mass spectrometry-based targeted proteomics, by which viral proteins can
be rapidly detected from complex samples down to the strain level with
high sensitivity and reproducibility. Developing such targeted assays
involves tedious steps of peptide candidate selection, peptide
synthesis, and assay optimization. Peptide selection requires extensive
preprocessing by comparing candidate peptides against a large search
space of background proteins. Purple (Picking Unique Relevant Peptides
for viraL Experiments) is a software tool for selecting target-specific
peptide candidates directly from given proteome sequence data.
Purple enables peptide candidate selection across various taxonomic
levels and filtering against backgrounds of varying complexity. Its
functionality is demonstrated using data from different virus species
and strains. Purple enables building taxon-specific targeted assays
and paves the way to time-efficient and robust viral diagnostics using
targeted proteomics.
This is the command line version of purple.
|
q2-composition
QIIME2 plugin for Compositional statistics
|
Versions of package q2-composition |
Release | Version | Architectures |
VCS | 2021.8.0+ds-1 | all |
|
License: BSD-3-clause
Debian package not available
Version: 2021.8.0+ds-1
|
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
researchers to start an analysis with raw DNA sequence data and finish with
publication-quality figures and statistical results.
Key features:
- Integrated and automatic tracking of data provenance
- Semantic type system
- Plugin system for extending microbiome analysis functionality
- Support for multiple types of user interfaces (e.g. API, command line,
graphical)
QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis
pipeline. QIIME 2 will address many of the limitations of QIIME 1, while
retaining the features that makes QIIME 1 a powerful and widely-used analysis
pipeline.
QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline.
New functionality will regularly become available through QIIME 2 plugins. You
can view a list of plugins that are currently available on the QIIME 2 plugin
availability page. The future plugins page lists plugins that are being
developed.
Please cite:
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso:
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
(eprint)
Nature Biotechnology
37
(2019)
|
q2-deblur
QIIME2 plugin to wrap the Deblur software for sequence quality control
|
Versions of package q2-deblur |
Release | Version | Architectures |
VCS | 2023.9.0-1 | all |
|
License: BSD-3-clause
Debian package not available
Version: 2023.9.0-1
|
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
researchers to start an analysis with raw DNA sequence data and finish with
publication-quality figures and statistical results.
Key features:
- Integrated and automatic tracking of data provenance
- Semantic type system
- Plugin system for extending microbiome analysis functionality
- Support for multiple types of user interfaces (e.g. API, command line,
graphical)
QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis
pipeline. QIIME 2 will address many of the limitations of QIIME 1, while
retaining the features that makes QIIME 1 a powerful and widely-used analysis
pipeline.
QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline.
New functionality will regularly become available through QIIME 2 plugins. You
can view a list of plugins that are currently available on the QIIME 2 plugin
availability page. The future plugins page lists plugins that are being
developed.
Please cite:
Amnon Amir, Daniel McDonald, Jose A. Navas-Molina, Evguenia Kopylova, James T. Morton, Zhenjiang Zech Xu, Eric P. Kightley, Luke R. Thompson, Embriette R. Hyde, Antonio Gonzalez and Rob Knight:
Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns.
(PubMed,eprint)
mSystems
2
(2017)
|
q2-diversity
QIIME2 plugin for core diversity analysis
|
Versions of package q2-diversity |
Release | Version | Architectures |
VCS | 2021.8.0-1 | all |
|
License: BSD-3-clause
Debian package not available
Version: 2021.8.0-1
|
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
researchers to start an analysis with raw DNA sequence data and finish with
publication-quality figures and statistical results. QIIME 2
currently supports an initial end-to-end microbiome analysis pipeline.
Functionality is made available through QIIME 2 plugins.
This plugin provides the means to statistically assess the diversity
of microbiota. This has direct clinical interest, since with whatever
we eat or have antibiotics applied, the survival of different groups
of bacteria/yeasts will be affected. From these relative abundances of
strains that constribute the microbiome, most prominently, comparisons
within a group of samples (or an individual) determines the alpha
diversity and between (groups of) samples the beta diversity is
inspected.
This package is key to most workflows in qiime.
Please cite:
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso:
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
(eprint)
Nature Biotechnology
37
(2019)
|
q2-gneiss
QIIME2 plugin for Compositional Data Analysis and Visualization
|
Versions of package q2-gneiss |
Release | Version | Architectures |
VCS | 2020.11.1-1 | all |
|
License: BSD-3-clause
Debian package not available
Version: 2020.11.1-1
|
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
researchers to start an analysis with raw DNA sequence data and finish with
publication-quality figures and statistical results.
Key features:
- Integrated and automatic tracking of data provenance
- Semantic type system
- Plugin system for extending microbiome analysis functionality
- Support for multiple types of user interfaces (e.g. API, command line,
graphical)
QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis
pipeline. QIIME 2 will address many of the limitations of QIIME 1, while
retaining the features that makes QIIME 1 a powerful and widely-used analysis
pipeline.
QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline.
New functionality will regularly become available through QIIME 2 plugins. You
can view a list of plugins that are currently available on the QIIME 2 plugin
availability page. The future plugins page lists plugins that are being
developed.
Please cite:
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso:
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
(eprint)
Nature Biotechnology
37
(2019)
|
q2-longitudinal
QIIME2 plugin for longitudinal studies and paired comparisons
|
Versions of package q2-longitudinal |
Release | Version | Architectures |
VCS | 2023.9.1+ds-1 | all |
|
License: BSD-3-clause
Debian package not available
Version: 2023.9.1+ds-1
|
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
researchers to start an analysis with raw DNA sequence data and finish with
publication-quality figures and statistical results.
Key features:
- Integrated and automatic tracking of data provenance
- Semantic type system
- Plugin system for extending microbiome analysis functionality
- Support for multiple types of user interfaces (e.g. API, command line,
graphical)
QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis
pipeline. QIIME 2 will address many of the limitations of QIIME 1, while
retaining the features that makes QIIME 1 a powerful and widely-used analysis
pipeline.
QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline.
New functionality will regularly become available through QIIME 2 plugins. You
can view a list of plugins that are currently available on the QIIME 2 plugin
availability page. The future plugins page lists plugins that are being
developed.
Please cite:
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso:
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
(eprint)
Nature Biotechnology
37
(2019)
|
q2-vsearch
QIIME 2 plugin for clustering and dereplicating with vsearch
|
Versions of package q2-vsearch |
Release | Version | Architectures |
VCS | 2023.9.0-1 | all |
|
License: BSD-3-clause
Debian package not available
Version: 2023.9.0-1
|
A QIIME 2 plugin that wraps the vsearch application, and provides
methods for clustering and dereplicating features and sequences.
|
qtlreaper
QTL analysis for expression data
|
Versions of package qtlreaper |
Release | Version | Architectures |
VCS | 1.1.1-1 | all |
|
License: GPL-2+
Debian package not available
Version: 1.1.1-1
|
QTL Reaper is software, written in C and compiled as a Python module, for
rapidly scanning microarray expression data for QTLs. It is essentially
the batch-oriented version of WebQTL. It requires, as input, expression
data from members of a set of recombinant inbred lines and genotype
information for the same lines. It searches for an association between
each expression trait and all genotypes and evaluates that association
by a permutation test. For the permutation test, it performs only as
many permutations as are necessary to define the empirical P-value to a
reasonable precision. It also performs bootstrap resampling to estimate
the confidence region for the location of a putative QTL.
The reaper module is used underneath the http://genenetwork.org site.
|
qualimap
evaluating next generation sequencing alignment data
|
Versions of package qualimap |
Release | Version | Architectures |
VCS | 2.2.1+dfsg-1 | all |
|
License: GPL-2+
Debian package not available
Version: 2.2.1+dfsg-1
|
Qualimap 2 provides both a Graphical User Interface (GUI) and a
command-line interface to facilitate the quality control of alignment
sequencing data and its derivatives like feature counts.
Supported types of experiments include:
- Whole-genome sequencing
- Whole-exome sequencing
- RNA-seq (speical mode available)
- ChIP-seq
Qualimap examines sequencing alignment data in SAM/BAM files according
to the features of the mapped reads and provides an overall view of the
data that helps to the detect biases in the sequencing and/or mapping of
the data and eases decision-making for further analysis.
Qualimap provides multi-sample comparison of alignment and counts data.
- Fast analysis accross the reference of genome coverage and nucleotide
distribution;
- Easy to interpret summary of the main properties of the
alignment data;
- Analysis of the reads mapped inside/outside of the regions provided
in GFF format;
- Computation and analysis of read counts obtained from intersectition
of read alignments with genomic features;
- Analysis of the adequasy of the sequencing depth in RNA-seq
experiments;
- Multi-sample comparison of alignment and counts data;
- Clustering of epigenomic profiles.
|
quast
Quality Assessment Tool for Genome Assemblies
|
Versions of package quast |
Release | Version | Architectures |
VCS | 5.0.2+dfsg-1 | all |
|
License: GPL-2
Debian package not available
Version: 5.0.2+dfsg-1
|
QUAST evaluates genome assemblies. For metagenomes, please see MetaQUAST
project. It works both with and without a given reference genome.
The tool accepts multiple assemblies, thus it allows for comparisons.
|
r-bioc-mofa2
Multi-Omics Factor Analysis v2
|
Versions of package r-bioc-mofa2 |
Release | Version | Architectures |
VCS | 1.2.2+ds-1 | all |
|
License: GPL-2+
Debian package not available
Version: 1.2.2+ds-1
|
The MOFA2 package contains a collection of tools for training and
analysing multi-omic factor analysis (MOFA). MOFA is a probabilistic
factor model that aims to identify principal axes of variation from data
sets that can comprise multiple omic layers and/or groups of samples.
Additional time or space information on the samples can be incorporated
using the MEFISTO framework, which is part of MOFA2. Downstream analysis
functions to inspect molecular features underlying each factor,
vizualisation, imputation etc are available.
|
r-bioc-org.mm.eg.db
genome wide annotation for Mouse
|
Versions of package r-bioc-org.mm.eg.db |
Release | Version | Architectures |
VCS | 3.11.4-1 | all |
|
License: Artistic-2.0
Debian package not available
Version: 3.11.4-1
|
Genome wide annotation for Mouse, primarily based on mapping using
Entrez Gene identifiers.
|
r-cran-drinsight
drug repurposing on transcriptome sequencing data
|
Versions of package r-cran-drinsight |
Release | Version | Architectures |
VCS | 0.1.1-1 | all |
|
License: GPL-2
Debian package not available
Version: 0.1.1-1
|
The package's name is an acronym for "Drug Repurposing Integration and
Systematic Investigation of Genomic High Throughput Data", which pretty
much describes it: This is a connectivity mapping-based drug repurposing
tool that identifies drugs that can potentially reverse query disease
phenotype or have similar functions with query drugs.
|
r-other-apmswapp
GNU R Pre- and Postprocessing For Affinity Purification Mass Spectrometry
|
Versions of package r-other-apmswapp |
Release | Version | Architectures |
VCS | 1.0-1 | all |
|
License: <license>
Debian package not available
Version: 1.0-1
|
The reliable detection of protein-protein-interactions by affinity
purification mass spectrometry (AP-MS) is a crucial stepping stone for
the understanding of biological processes. The main challenge in a
typical AP-MS experiment is to separate true interaction proteins from
contaminants by contrasting counts of proteins binding to specific baits
with counts of negative controls.
|
r-other-fastbaps
A fast genetic clustering algorithm that approximates a Dirichlet Process Mixture model
|
Versions of package r-other-fastbaps |
Release | Version | Architectures |
VCS | 1.0.4-1 | all |
|
License: MIT
Debian package not available
Version: 1.0.4-1
|
Takes a multiple sequence alignment as input and clusters according to the 'no-admixture' model.
It combines ideas from the Bayesian Hierarchical Clustering algorithm of Heller et al.
and hierBAPS to produce a rapid and accurate clustering algorithm.
|
raxml-ng
phylogenetic tree inference tool which uses maximum-likelihood
|
Versions of package raxml-ng |
Release | Version | Architectures |
VCS | 1.0.1-1 | all |
|
License: AFFERO-3
Debian package not available
Version: 1.0.1-1
|
RAxML Next Generation: faster, easier-to-use and more flexible
RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood
(ML) optimality criterion. Its search heuristic is based on iteratively
performing a series of Subtree Pruning and Regrafting (SPR) moves, which
allows to quickly navigate to the best-known ML tree. RAxML-NG is a successor
of RAxML (Stamatakis 2014) and leverages the highly optimized likelihood
computation implemented in libpll (Flouri et al. 2014).
RAxML-NG offers improvements in speed, flexibility and user-friendliness
over the previous RAxML versions. It also implements some of the
features previously available in ExaML (Kozlov et al. 2015), including
checkpointing and efficient load balancing for partitioned alignments.
|
repeatmasker
screen DNA sequences for interspersed repeats
|
Versions of package repeatmasker |
Release | Version | Architectures |
VCS | 4.0.7-1 | all |
|
License: OpenSoftwareLicense-2.1
Debian package not available
Version: 4.0.7-1
|
RepeatMasker is a program that screens DNA sequences for interspersed
repeats and low complexity DNA sequences. The output of the program is
a detailed annotation of the repeats that are present in the query
sequence as well as a modified version of the query sequence in which
all the annotated repeats have been masked (default: replaced by
Ns). Sequence comparisons in RepeatMasker are performed by the program
cross_match, an efficient implementation of the Smith-Waterman-Gotoh
algorithm developed by Phil Green, or by WU-Blast developed by Warren
Gish.
|
roadtrips
case-control association testing with unknown population and pedigree structure
|
Versions of package roadtrips |
Release | Version | Architectures |
VCS | 2.0+dfsg-1 | all |
|
License: GPL-3+
Debian package not available
Version: 2.0+dfsg-1
|
ROADTRIPS performs single-SNP, case-control association testing in
samples with partially or completely unknown population and pedigree
structure. ROADTRIPS uses an empirical covariance matrix calculated from
genomewide SNP data to correct for unknown population and pedigree
structure, while maintaining high power by taking advantage of known
pedigree information when it is available. The program is applicable to
association studies with completely general combinations of related and
unrelated individuals. Analysis can be performed genomewide (currently
just for autosomes).
ROADTRIPS is suitable for applications such as:
- correcting for possible population structure and/or misspecified
relationships in the context of case-control association testing in
samples of unrelated individuals and/or related individuals with well-
characterized pedigrees
- case-control association testing in samples from isolated populations
for which pedigree information is limited or unavailable
|
rosa
Removal of Spurious Antisense in biological RNA sequences
|
Versions of package rosa |
Release | Version | Architectures |
VCS | 1.0-1 | all |
|
License: GPL-3.0+
Debian package not available
Version: 1.0-1
|
In stranded RNA-Seq experiments it is possible to detect and
measure antisense transcription, important since antisense transcripts
impact gene transcription in several different ways. Stranded RNA-Seq
determines the strand from which an RNA fragment originates, and so can
be used to identify where antisense transcription may be implicated in
gene regulation.
However, spurious antisense reads are often present in experiments, and
can manifest at levels greater than 1% of sense transcript levels. This
is enough to disrupt analyses by causing false antisense counts to
dominate the set of genes with high antisense transcription levels.
The RoSA (Removal of Spurious Antisense) tool detects the presence of
high levels of spurious antisense transcripts, by:
- analysing ERCC spike-in data to find the ratio of antisense:sense
transcripts in the spike-ins; or
- using antisense and sense counts around splice sites to provide a
set of gene-specific estimates; or
- both.
Once RoSA has an estimate of the spurious antisense, expressed as a
ratio of antisense:sense counts, RoSA will calculate a correction to
the antisense counts based on the ratio. Where a gene-specific estimate
is available for a gene, it will be used in preference to the global
estimate obtained from either spike-ins or spliced reads.
This package provides the library for the statistics suite R.
|
rsat
Regulatory Sequence Analysis Tools
|
Versions of package rsat |
Release | Version | Architectures |
VCS | 2016-03-14+dfsg-1 | all |
|
License: <license>
Debian package not available
Version: 2016-03-14+dfsg-1
|
RSAT is a series of modular computer programs specifically designed for
the detection of regulatory signals in non-coding sequences.
RSAT servers have been up and running since 1997. The project was
initiated by Jacques van Helden, and is now pursued by the RSAT team.
Please cite:
Alejandra Medina-Rivera, Matthieu Defrance, Olivier Sand, Carl Herrmann, Jaime A. Castro-Mondrago, Jeremy Delerce, Sébastien Jaeger, Christophe Blanchet, Pierre Vincens, Christophe Caron, Daniel M. Staines, Bruno Contreras-Moreira, Marie Artufel, Lucie Charbonnier-Khamvongsa, Céline Hernandez, Denis Thieffry, Morgane Thomas-Chollier and Jacques van Helden:
RSAT 2015: Regulatory Sequence Analysis Tools.
(PubMed,eprint)
Nucleic Acids Res.
43(W1):W50-W56
(2015)
|
sailfish
RNA-seq expression estimation
|
Versions of package sailfish |
Release | Version | Architectures |
VCS | 0.10.1+dfsg-1 | all |
|
License: GPL-3.0+
Debian package not available
Version: 0.10.1+dfsg-1
|
RNA-seq is a technology to read at least parts of individual RNA
sequences of a tissue sample. After assigning these reads to genes
that are likely responsible to have coded for them (mapping), this
gives an insight (estimate) about how much these genes have been
active (expressed) in that sample. The trickier bits in that process
to address is the similarity of genes and the genes being capable to
variably but deterministically skip parts of their sequence to be read
(introns). A single variantly spliced gene may then yield different
sequences (isoforms) and the RNA-seq evaluation better informs about
this. It may be relevant for a disease.
Sailfish is particularly good (efficient) in this process. It tricks
the complexity by introducing an intermediate level of artificial very
short reads to which the alternative splicing is of no concern. That
can then be addressed by "telephone-book"-like hashing techniques that
are easy and lightning fast. The final presentation is then found to
be competitive with established mappers like eXpress and Cufflinks.
|
sap
Pairwise protein structure alignment via double dynamic programming
|
Versions of package sap |
Release | Version | Architectures |
VCS | 1.1.3-1 | all |
|
License: GPL-3.0+
Debian package not available
Version: 1.1.3-1
|
In contrast to DNA, proteins exhibit an apparently unlimited variety of
structure. This is a necessary requirement of the vast array of
differing functions that they perform in the maintainance of life,
again, in contrast to the relatively static archival function of DNA.
Not only do we observe a bewildering variety of form but even within a
common structure, there is variation in the lengths and orientation
substructures. Such variation is both a reflection on the very long time
periods over which some structures have diverged and also a consequence
of the fact that proteins cannot be completely rigid bodies but must
have flexibility to accommodate the structural changes that are almost
always necessary for them to perform their functions. These aspects make
comparing structure and finding structural similarity over long
divergence times very difficult. Indeed, computationally, the problem of
recognizing similarity is one of three-dimensional pattern recognition,
which is a notoriously difficult problem for computers to perform. In
this chapter, guidance is provided on the use of a flexible structure
comparison method that overcomes many of the problems of comparing
protein structures that may exhibit only weak similarity.
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seq-seq-pan
workflow for the SEQuential alignment of SEQuences
|
Versions of package seq-seq-pan |
Release | Version | Architectures |
VCS | 1.0.1-1 | all |
|
License: BSD-2-clause
Debian package not available
Version: 1.0.1-1
|
Seq-seq-pan is a framework that provides methods for adding or removing
new genomes from a set of aligned genomes and uses these to construct a
whole genome alignment. Throughout the sequential workflow the alignment
is optimized for generating a representative linear presentation of the
aligned set of genomes, that enables its usage for annotation and in
downstream analyses.
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seqwish
alignment to variation graph inducer
|
Versions of package seqwish |
Release | Version | Architectures |
VCS | 0.7.1-1 | all |
|
License: MIT
Debian package not available
Version: 0.7.1-1
|
Seqwish implements a lossless conversion from pairwise alignments
between sequences to a variation graph encoding the sequences and their
alignments. As input we typically take all-versus-all alignments, but
the exact structure of the alignment set may be defined in an
application specific way. This algorithm uses a series of disk-backed
sorts and passes over the alignment and sequence inputs to allow the
graph to be constructed from very large inputs that are commonly
encountered when working with large numbers of noisy input sequences.
Memory usage during construction and traversal is limited by the use of
sorted disk-backed arrays and succinct rank/select dictionaries to
record a queryable version of the graph.
|
signalalign
HMM-HDP models for MinION signal alignments
|
Versions of package signalalign |
Release | Version | Architectures |
VCS | 0.0+git20170131.3293fad+dfsg-1 | all |
|
License: MIT
Debian package not available
Version: 0.0+git20170131.3293fad+dfsg-1
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MinION signal-level alignment and methylation detection using hidden
Markov Models with hierarchical Dirichlet process kmer learning.
Nanopore sequencing is based on the principal of isolating a nanopore in
a membrane separating buffered salt solutions, then applying a voltage
across the membrane and monitoring the ionic current through the
nanopore. The Oxford Nanopore Technologies (ONT) MinION sequences DNA by
recording the ionic current as DNA strands are enzymatically guided
through the nanopore. SignalAlign will align the ionic current from the
MinION to a reference sequence using a trainable hidden Markov model
(HMM). The emissions model for the HMM can either be the table of
parametric normal distributions provided by ONT or a hierarchical
Dirichlet process (HDP) mixture of normal distributions. The HDP models
enable mapping of methylated bases to your reference sequence.
|
sina
reference based multiple sequence alignment
|
Versions of package sina |
Release | Version | Architectures |
VCS | 1.6.1-1 | all |
|
License: <license>
Debian package not available
Version: 1.6.1-1
|
SINA is a tool to add sequences to an existing multiple sequence
alignment. It needs about 1 second on a single core to add one 16S full
length sequence (about 100k/h on a 32-core workstation). It was
developed to create the multi-million sequence alignment that is the
core of the SILVA SSU and LSU rRNA databases.
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sistr
Salmonella In Silico Typing Resource (SISTR)
|
Versions of package sistr |
Release | Version | Architectures |
VCS | 1.0.2-1 | all |
|
License: Apache-2.0
Debian package not available
Version: 1.0.2-1
|
The Salmonella In Silico Typing Resource (SISTR) commandline tool allows
serovar predictions from whole-genome sequence assemblies by
determination of antigen gene and cgMLST gene alleles using BLAST. Mash
MinHash can also be used for serovar prediction.
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situs
Modeling of atomic resolution structures into low-resolution density maps
|
Versions of package situs |
Release | Version | Architectures |
VCS | 2.7.2-1 | all |
|
License: GPL.
Debian package not available
Version: 2.7.2-1
|
Situs is an award-winning program package for the modeling of atomic resolution
structures into low-resolution density maps e.g. from electron microscopy,
tomography, or small angle X-ray scattering. The software supports both
rigid-body and flexible docking using a variety of fitting strategies. Situs is
developed by Willy Wriggers and collaborators: biomachina.org.
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sparta
automated reference-based bacterial RNA-seq Transcriptome Analysis
|
Versions of package sparta |
Release | Version | Architectures |
VCS | 1.01+dfsg-1 | all |
|
License: free
Debian package not available
Version: 1.01+dfsg-1
|
SPARTA is a workflow aimed at analyzing single-end Illumina RNA-seq
data. The workflow combines several tools: Trimmomatic (read
trimming/adapter removal), FastQC (read quality analysis), Bowtie
(mapping reads to the reference genome), HTSeq (transcript/gene feature
abundance counting), and edgeR (differential gene expression analysis).
Within the differential gene expression analysis step, batch effects can
be detected and the user is warned of the potential, unintended
additional variable. The analysis procedure is outlined below.
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ssaha
Sequence Search and Alignment by Hashing Algorithm
|
Versions of package ssaha |
Release | Version | Architectures |
VCS | 3.1c-1 | all |
|
License: GPL-2+
Debian package not available
Version: 3.1c-1
|
SSAHA is a software tool for very fast matching and alignment of DNA
sequences. It achieves its fast search speed by converting sequence
information into a `hash table' data structure, which can then be
searched very rapidly for matches.
SSAHA is the only free software of its category (fast search of nearly
indentical sequences). The popular alternative, BLAT, is restricted to
non-commercial use.
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strap
Comfortable and intuitive protein alignment editor / viewer
|
Versions of package strap |
Release | Version | Architectures |
VCS | 1.1.3-1 | all |
|
License: free
Debian package not available
Version: 1.1.3-1
|
Strap is started from the menu "Science" in the "Applications" menu
or with the shell command strap_protein_alignment. Alignments can be
manually edited or computed automatically using sequence and/or
structure based methods. Information can be attached to proteins and
residue selections such as free text notes, balloon messages,
cross-references as well as 3D and PDF display styles. Alignments
can be exported in several formats: Multiple-Fasta, ClustalW, MSF,
HSSP, Jalview. Decorated alignments with residue annotations and
secondary structure cartoons can be exported to PDF, HTML and
Word-processors to create figures in publication quality - see
http://3d-alignment.eu/ for details. Strap is an integrated
environment for Bioinformatics tools and resources like DAS sequence
features, 3D-visualization, structure prediction and Blast search. It
is scriptable and extendable and can be used by other programs to
display sequence alignments and 3D-superpositions.
|
strap-base
essential files for the interactive alignment viewer and editor Strap
|
Versions of package strap-base |
Release | Version | Architectures |
VCS | 1.1.3-1 | all |
|
License: free
Debian package not available
Version: 1.1.3-1
|
Most users should install the package strap which in addition
installs required Debian packages for alignment computation and 3D
visualization. Strap-base provides utilities for protein and
alignment file format conversion: strap_to_clustal, strap_to_msf,
strap_to_fasta, strap_to_multiple_fasta. It also provides
interactive alignment visualization and HTML export for other
bioinformatics software. The command strap_base with the option
-script=file or -script=named_pipe opens a new interactive alignment
view. Named pipes are the basis for interprocess communication. The
command strap_to_html is a command line tool to produce
decorated and annotated alignments suitable for web-browsers with
script commands as explained in
http://www.bioinformatics.org/strap/alignment-to-html.html.
|
strelka
strelka2 germline and somatic small variant caller
|
Versions of package strelka |
Release | Version | Architectures |
VCS | 2.9.10+dfsg-1 | all |
|
License: GPL-3+
Debian package not available
Version: 2.9.10+dfsg-1
|
Strelka2 is a fast and accurate small variant caller optimized for
analysis of germline variation in small cohorts and somatic variation in
tumor/normal sample pairs. The germline caller employs an efficient
tiered haplotype model to improve accuracy and provide read-backed
phasing, adaptively selecting between assembly and a faster alignment-
based haplotyping approach at each variant locus. The germline caller
also analyzes input sequencing data using a mixture-model indel error
estimation method to improve robustness to indel noise. The somatic
calling model improves on the original Strelka method for liquid and late-
stage tumor analysis by accounting for possible tumor cell contamination
in the normal sample. A final empirical variant re-scoring step using
random forest models trained on various call quality features has been
added to both callers to further improve precision.
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tab2mage
submitting large microarray experiment datasets to public repository database
|
Versions of package tab2mage |
Release | Version | Architectures |
VCS | 20080626-1 | all |
|
License: free
Debian package not available
Version: 20080626-1
|
Tab2MAGE is a software package written and supported by the ArrayExpress
curation team, which aims to ease the process of submitting large
microarray experiment datasets to our public repository database. To
this end, Tab2MAGE currently includes two tools, the tab2mage.pl script
itself, and a data file checking script, expt_check.pl. With these
scripts it is possible to perform an initial data file validation
against an array design (e.g., in the form of an "Array Description
File" or ADF), and then to generate MAGE-ML using these data files
alongside a separate spreadsheet providing MIAME-compliant sample
annotation.
|
tacg
command line program for finding patterns in nucleic acids
|
Versions of package tacg |
Release | Version | Architectures |
VCS | 4.1-1 | all |
|
License: GPL+additions
Debian package not available
Version: 4.1-1
|
tacg is a character-based, command line tool for unix-like operating systems
for pattern-matching in nucleic acids and performing some of the basic protein
manipulations. It was originally designed for restriction enzyme analysis of
DNA, but has been extended to other types of matching. It now handles
degenerate sequence input in a variety of matching approaches, as well as
patterns with errors, regular expressions and TRANSFAC-formatted matrices.
It was designed to be a grep for DNA and like the original grep, its
capabilities have grown so that now the author has to keep calling up the help
page to figure out which flags (now ~50) mean what. tacg is NOT a GUI
application in any sense. However, it's existance as a strictly command-line
tool lends itself well to Webification and wrapping by various GUI tools and
it is now distributed with a web interface form and a Perl CGI handler.
Additionally, it can easily be integrated into editors that support shell
commands such as nedit.
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tandem-genotypes
compare lengths of duplications in DNA sequences
|
Versions of package tandem-genotypes |
Release | Version | Architectures |
VCS | 1.8.3-1 | all |
|
License: GPL-3.0+
Debian package not available
Version: 1.8.3-1
|
Only a fraction of the DNA in the human genome (and that of other species
that are not optimised for the speed of their replication like viruses)
are coding for genes. Other parts may be binding to transcription factors
or direct the expression of genes in other ways - these other bits may
not be fully understood, and parts may indeed be "junk", but this is
only until user finds a clinical feature to be statistically associated
with something statistically noteworthy in the DNA sequences.
Features that somehow seem informative when looking at the DNA are
whatever does not look like random. This tool looks at a special case
of repeats - short regions that are duplicated, i.e. they appear as a
tandem. When these repeats are longer, then these would be referred as
microsatellites.
When interested in structural variations, within a family/population or
to compare cancer tissue with benign samples, you may also want to look
at these repeats. This software determines the lengths (and changes to
the lengths) across samples and knows how to present this graphically.
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tide
SEQUEST Searching for Peptide Identification from Tandem Mass Spectra
|
Versions of package tide |
Release | Version | Architectures |
VCS | 0.0.r15918-1 | all |
|
License: Apache-2.0
Debian package not available
Version: 0.0.r15918-1
|
Tide implements the SEQUEST algorithm for peptide identification and
that achieves a dramatic speedup over Crux and SEQUEST. The
optimization strategies detailed here employ a combination of
algorithmic and software engineering techniques to achieve speeds up to
170 times faster than a recent version of SEQUEST that uses indexing.
For example, on a single Xeon CPU, Tide searches 10,000 spectra against
a tryptic database of 27,499
C.\ elegans proteins at a rate of 1,550 spectra per second, which
compares favorably with a rate of 8.8 spectra per second for a recent
version of SEQUEST with index running on the same hardware.
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tigr-glimmer-mg
finding genes in environmental shotgun DNA sequences
|
Versions of package tigr-glimmer-mg |
Release | Version | Architectures |
VCS | 0.3.2-1 | all |
|
License: free
Debian package not available
Version: 0.3.2-1
|
Glimmer-MG is a system for finding genes in environmental shotgun DNA
sequences. Glimmer-MG (Gene Locator and Interpolated Markov ModelER -
MetaGenomics) uses interpolated Markov models (IMMs) to identify the
coding regions and distinguish them from noncoding DNA.
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tn-seqexplorer
explore and analyze Tn-seq data for prokaryotic genomes
|
Versions of package tn-seqexplorer |
Release | Version | Architectures |
VCS | 1.5+dfsg-1 | all |
|
License: GPL
Debian package not available
Version: 1.5+dfsg-1
|
Tn-seq Explorer allows users to explore and analyze Tn-seq data for
prokaryotic (bacterial or archaeal) genomes. It implements two
alternative methods for identification of essential genes and provides
additional tools to investigate the Tn-seq data. The primary goal of the
data analysis is to study fitness by identifying genes that are essentia
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ufasta
utility to manipulate fasta files
|
Versions of package ufasta |
Release | Version | Architectures |
VCS | 0.0.3+git20190131.85d60d1-1 | all |
|
License: to_be_clarified
Debian package not available
Version: 0.0.3+git20190131.85d60d1-1
|
Description of ufasta subcommands:
- one: remove the new lines in the data section. Hence, all the
sequences are written on one line. In some sense, it is the opposite
of the format subcommand.
- format: reformat the data sections. The data is written in lines of
the same length, it can changes the content in upper/lower case.
- sizes: print the amount of sequence in each section
- head: like UNIX head. Display the first 10 sequences
- tail: like UNIX tail. Display the last 10 sequences
- rc: reverse complement every sequence
- n50, stats: display stats about the sequences: N50, E size, total
size, etc.
- extract: extract a sequence whose header match given names
- hsort, sort: sort file based on header content
- dsort: sort the data sections
- hgreap: output sequences whose header match the regular expression
- dgresp: output sequences whose sequence match the regular expression
- split: split a fasta file into many files
|
umap
quantify genome and methylome mappability
|
Versions of package umap |
Release | Version | Architectures |
VCS | 1.0.0-1 | all |
|
License: GPL-3.0
Debian package not available
Version: 1.0.0-1
|
Umap identifies uniquely mappable regions of any genome. Its Bismap
extension identifies mappability of the bisulfite converted
genome (methylome).
|
unc-fish
Fast Identification of Segmental Homology
|
Versions of package unc-fish |
Release | Version | Architectures |
VCS | 1.0+dfsg-1 | all |
|
License: LicenseAgreementFISH
Debian package not available
Version: 1.0+dfsg-1
|
FISH is software for identifying regions of common ancestry between
genome maps. Fast identification and statistical evaluation of
segmental homologies in comparative maps.
Development and maintenance of FISH is supported by funding from the
National Science Foundation (Plant Genome Research Program Grants
DBI-0110069 and DBI-0227314 to TJV and DMS-0102008 to PPC).
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varmatch
robust matching of small genomic variant datasets
|
Versions of package varmatch |
Release | Version | Architectures |
VCS | 0+git20180126.5c6fed5+dfsg-1 | all |
|
License: GPL-3.0+
Debian package not available
Version: 0+git20180126.5c6fed5+dfsg-1
|
Small variant calling is an important component of many analyses, and, in
many instances, it is important to determine the set of variants which appear
in multiple callsets. Variant matching is complicated by variants that have
multiple equivalent representations. Normalization and decomposition
algorithms have been proposed, but are not robust to different
representation of complex variants. The VarMatch algorithm is robust to
different representation of complex variants and is particularly effective
in low complexity regions or those dense in variants. VarMatch also provides
summary statistics, annotations, and visualizations that are useful for
understanding callers' performance.
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vmd
presentation of traces of molecular dynamics runs
|
Versions of package vmd |
Release | Version | Architectures |
VCS | 1.9.1-3 | all |
|
License: University_of_Illinois_non-free
Debian package not available
Version: 1.9.1-3
|
VMD stands for Visual Molecular Dynamics. While text books
and even structure databases because of technical problems only
present static pictures of proteins or DNA, for the understanding
of the properties of those molecules their vibration or their
movement in general is important.
The movements itself are calculated by molecular dynamics programs,
such as NAMD (by the same group), Rosetta, BALLView or GROMACS. The
latter two are already in the distribution, we have package build
instructions for Rosetta.
VMD has a series of nice features, from displaying through animation
to analysing. It can be scripted, clustered, and runs on all common OS.
Its license does not allow to redistribute a Debian package. But
to share these build instructions for such a package is just fine.
|
zodiac-zeden
ZODIAC - Zeden's Organise DIsplay And Compute
|
Versions of package zodiac-zeden |
Release | Version | Architectures |
VCS | 0.6.5-1 | all |
|
License: GPL-3.0+
Debian package not available
Version: 0.6.5-1
|
Zodiac is a molecular modelling suite for computation, analysis and display of
molecular data. It features state-of-the-art tools for managing molecular
databases, run molecular docking experiments, compute raytraced images
and much more.
|
Unofficial packages built by somebody else
big-blast
Helper tool to run blast on large sequences
|
|
License: not specified
|
This script will chop up a large sequence, run blast on each bit and
then write out an EMBL feature table and a MSPcrunch -d file
containing the hits.
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estferret
processes, clusters and annotates EST data
|
|
License: to be clarified
|
ESTFerret processes, clusters and annotates EST data. It is
user-configurable. Results are currently stored in a series of text
tables. Annotation consists of searches against use r-defined blast
databases, prosite, GO and allocation of EC numbers where possible.
EST-ferret is a user-configurable, automated pipeline for the
convenient analysis of EST sequence data that includes all of the
necessary steps for cleanup and trimming, submission to external
sequence repositories, clustering, identification by BLAST homology
searches and by searches of protein domain databases, annotation with
computer-addressable terms and production of outputs for direct entry
into microarray analysis packages. It is composed of several widely
used, open-source algorithms, including PHRED, CAP3, BLAST, and a
range of sequence and annotation databases, including Gene Ontology
and Conserved Domain Database to deliver a putative identity and a
detailed annotation of each clone. It can be run either step-by-step
to track the outputs, or as a single batch process. Users can easily
edit the configuration file to define parameter settings.
This package has five major components: (1) ESTs coding system; (2)
sequence processing; (3) sequence clustering; (4) sequence annotating
and (5) storage and reporting of results. DNA trace files are renamed
and converted into FASTA format, cleaned and submitted to
dbEST(Boguski, et al, 1993). Sequence assembly uses two rounds of
CAP3 to assemble the ESTs into groups corresponding to separate gene
families and unique genes. Sequence identification and annotation is
provided by a series of BLAST homology searches (Parallel_BLAST and
Priority_BLAST) against user-defined sequence databases implemented
with the NCBI BLASTALL algorithm. The BLAST results are parsed and
annotation terms that reflect functional attributes are captured from
Gene Ontology (The Gene Ontology Consortium, 2000), KEGG and Enzyme
Commission (EC) databases and applied to each of the clones. CDD (and
InterPro) searches are performed for seeking protein domains in the
sequences. Other options are provided to run PatSearch, RepeatMasker
and BLAT to find UTRs, repeats and EST candidates in
genomes. Finally, the package generates analysis reports in a variety
of flat file formats, sources of which can be serve as inputs for
some gene annotation and gene expression profiling tools, and also as
a MySQL database or web-browsable search tool.
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maxd
data warehouse and visualisation environment for genomic expression data
|
|
License: Artistic
|
Maxd is a data warehouse and visualisation environment for genomic
expression data. It is being developed in the University of
Manchester by the Microarray Bioinformatics Group.
Software components:
maxdLoad2 - standards-compliant, highly customisable transcriptomics
database
maxdView - modular and easily extensible data visualisation and
analysis environment
maxdSetup - installation management utility
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migrate
estimation of population sizes and gene flow using the coalescent
|
|
License: to be clarified
|
Migrate estimates effective population sizes and past migration rates
between n population assuming a migration matrix model with
asymmetric migration rates and different subpopulation sizes. Migrate
uses maximum likelihood or Bayesian inference to jointly estimate all
parameters. It can use the followind data types: sequence data using
Felsenstein's 84 model with or without site rate variation, single
nucleotide polymorphism data, microsatellite data using a stepwise
mutation model or a brownian motion mutation model, and
electrophoretic data using an 'infinite' allele model. The output can
contain: Estimates of all migration rates and all population sizes,
assuming constant mutation rates among loci or a gamma distributed
mutation rate among loci. Profile likelihood tables, Percentiles,
Likelihood-ratio tests, and simple plots of the log-likelihood
surfaces for all populations and all loci.
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msatfinder
identification and characterization of microsatellites in a comparative genomic context
|
|
License: GPL
|
Msatfinder is a Perl script designed to allow the identification and
characterization of microsatellites in a comparative genomic
context. There is also an online manual, a discussion forum and an
online interface where users can do searches in any number of DNA or
protein sequences (as long as the maximum size of all sequences does
not exceed 10MB). Nucleotide and amino acid sequences in GenBank,
FASTA, EMBL and Swissprot formats are supported.
|
oligoarrayaux
Prediction of Melting Profiles for Nucleic Acids
|
|
License: non-free (fre academical use)
|
OligoArrayAux is a subset of the UNAFold package for use with
OligoArray (http://berry.engin.umich.edu/oligoarray2_1/). OligoArray
is a free software that computes gene specific oligonucleotides for
genome-scale oligonucleotide microarray construction. (It is not
really specified what they mean with "free software". You can
download the source code after registration: "registration is the
only way for me to keep trace of OligoArray users and be able to send
you a bug fix or a new release".)
The original UNAFold server is available at
http://dinamelt.bioinfo.rpi.edu/download.php and you should probably
read http://dinamelt.bioinfo.rpi.edu/ if you want to know more about
"Prediction of Melting Profiles for Nucleic Acids".
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partigene
generating partial gemomes
|
|
License: GPL
|
PartiGene is part of the Edinburgh-EGTDC developed EST-software
pipeline at the moment consisting of trace2dbEST, PartiGene,
wwwPartiGene, port4EST and annot8r. PartiGene is a menu-driven,
multi-step software tool which takes sequences (usually ESTs) and
creates a dataabase of a non-redundant set of sequence objects
(putative genes) which we term a partial genome.
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pfaat
Protein Family Alignment Annotation Tool
|
|
License: GPL
|
Pfaat is a Java application that allows one to edit, analyze, and
annotate multiple sequence alignments. The annotation features are a
key component as they provide a framework to for further sequence,
structure and statistical analysis.
|
prot4est
EST protein translation suite
|
|
License: GPL
|
prot4EST is a perl script that takes expressed sequence tags (ESTs)
and translates them optimally to produce putative peptides. prot4EST
intergrates a number of programs to overcome problems inherent with
translating ESTs.
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python3-orange
|
|
License: GPLv3
|
Orange is a component-based data mining software. It includes a range
of data visualization, exploration, preprocessing and modeling
techniques. It can be used through a nice and intuitive user interface
or, for more advanced users, as a module for Python programming language.
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qtlcart
map quantitative traits using a map of molecular markers
|
|
License: GPL
|
QTL Cartographer is a suite of programs to map quantitative traits
using a map of molecular markers. It contains a set of programs that
will aid in locating the genes that control quantitative traits using
a molecular map of markers. It includes some programs to allow
simulation studies of experiments.
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rbs-finder
find ribosome binding sites(RBS)
|
|
License: not specified
|
The program implements an algorithm to find ribosome binding
sites(RBS) in the upstream regions of the genes annotated by
Glimmer2, GeneMark, or other prokaryotic gene finders. If there is
no RBS-like patterns in this region, program searches for a start
codon having a RBS-like pattern ,in the same reading frame upstream
or downstream and relocates start codon accordingly.
You can find more detailed information at
http://nbc11.biologie.uni-kl.de/docbook/doc_userguide_bioinformatics_server/chunk/ch01s06.html
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roche454ace2caf
convert GS20 or FLX assemblies into CAF format
|
|
License: not specified
|
Some tools to convert GS20 or FLX assemblies (454Contigs.ace) into
CAF format so that these are correct viewable/editable/... whithin
the staden package (gap4). You have then access to "hidden data",
exact aligned trace and there positions, base values etc and whith
staden-1-7-0 you have graphical access to the associated flowgramm
traces (SFF format).
Description, Goals - please take a look at
http://genome.imb-jena.de/software/roche454ace2caf/Poster_UserMeeting_GS20_Munich_070328.pdf
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splitstree
Analyzing and Visualizing Evolutionary Data
|
|
License: to be clarified
|
Evolutionary data is most often presented as a phylogentic tree, the
underlying assumption being that evolution is a branching
process. However, real data is never ideal and thus doesn't always
support a unique tree, but often supports more than one possible
tree. Hence, it makes sense to consider tree reconstruction methods
that produce a tree, if the given data heavily favors one tree over
all others, but otherwise produces a more general graph that
indicates different possible phylogenies. One such method is the
Split Decomposition introduced by Hans-Juergen Bandelt and Andreas
Dress (1992) and its variations. Another example is Spectral Analysis
developed by Hendy, Penny and others.
These and other methods are implemented in the program SplitsTree,
that I wrote with contributions from Dave Bryant, Mike Hendy, Holger
Paschke, Dave Penny and Udo Toenges. It is based on the Nexus
format.
Note: There is a new version 4.0 written from scratch at
http://www.splitstree.org/ which requires a license key - so this is
probably non-free. Version 3.2 which is linked above has some
downloadable source code without any license or copyright statement -
so it has to be clarified whether we are able to distribute this code
or not.
|
taverna
designing and executing myGrid workflows for bioinformatics
|
|
License: LGPL
|
The Taverna workbench is a free software tool for designing and
executing workflows, created by the myGrid project, and funded
through OMII-UK. Taverna allows users to integrate many different
software tools, including web services, such as those provided by the
National Center for Biotechnology Information, The European
Bioinformatics Institute, the DNA Databank of Japan (DDBJ), SoapLab,
BioMOBY and EMBOSS.
The Taverna Workbench provides a desktop authoring environment and
enactment engine for scientific workflows expressed in Scufl (Simple
Conceptual Unified Flow language). The Taverna enactment engine is
also available separately, and other Scufl enactors are available
including Moteur. The myExperiment social web site supports finding
and sharing of workflows and has special support for Scufl
workflows. The Taverna workbench, myExperiment and associated
components are developed and maintained by the myGrid team, in
collaboration with the open source community.
|
taxinspector
browser for entries in the NCBI taxonomy
|
|
License: Artistic + other free licenses
|
TaxInspector is a browser for entries in the NCBI taxonomy. It is
designed to run as a plugin to annotation software such as maxdLoad2
and Pedro, but also has a standalone mode.
|
tetra
tetranucleotide frequency calculator
|
|
License: free academic
|
The TETRA program can be used to calculate how well tetranucleotide
usage patterns in DNA sequences correlate. Such correlations can
provide valuable hints on the relatedne ss of DNA sequences, and are
particularly useful for metagenomic sequences.
|
No known packages available but some record of interest (WNPP bug)
biomolecule Toolkit C++ library
|
|
License: GPL
Debian package not available
|
The Biomolecule Toolkit is a library for modeling biological
macromolecules such as proteins, DNA and RNA. It provides a C++ interface
for common tasks in structural biology to facilitate the development of
molecular modeling, design and analysis tools.
|
The microRNA sequence database
|
|
License: Public Domain
Debian package not available
|
The miRBase Sequence Database provides a searchable repository
for published microRNA sequences and associated annotation,
functionality previously provided by the microRNA Registry. miRBase
also contains predicted miRNA target genes in miRBase Targets, and
provides a gene naming and nomenclature function in the miRBase
Registry.
Release 9.1 of the database contains 4449 entries representing hairpin
precursor miRNAs, expressing 4274 mature miRNA products, in primates,
rodents, birds, fish, worms, flies, plants and viruses.
This package will install the miRBase database for mySQL, EMBOSS, and/or
ncbi-blast if you have the corresponding packages installed.
It is possible that mirbase will not be a package from the main archive, but
will be autogenerated as part of a larger data packaging effort.
|
Graphical interface for molecular phylogenetic inference
|
|
License: unknown
Debian package not available
|
Phylo_win is a graphical colour interface for molecular phylogenetic
inference. It performs neighbor-joining, parsimony and maximum
likelihood methods and bootstrap with any of them. Many distances can be
used including Jukes & Cantor, Kimura, Tajima & Nei, HKY, Galtier & Gouy
(1995), LogDet for nucleotidic sequences, Poisson correction for protein
sequences, Ka and Ks for codon sequences. Species and sites to include
in the analysis are selected by mouse. Reconstructed trees can be drawn,
edited, printed, stored and evaluated according to numerous criteria.
This program uses sources files from the Phylip program, which forbids
its use for profit. Therfore, Phylo_win will unfortunately have to be
distributed in contrib or non-free.
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No known packages available
amoscmp
comparative genome assembly package
|
|
License: Artistic
Debian package not available
|
A comparative assembler is a program that can assemble a set of
shotgun reads from an organism by mapping them to the finished
sequence of a related organism. Thus, a comparative assembler
transforms the traditional overlap-layout-consensus approach to
alignment-layout-consensus. The AMOScmp package uses the MUMmer
program to perform a mapping of the reads to the reference genome,
then processes the alignment results with a sophisticated layout
program designed to take into account polymorphisms between the two
genomes. For a detailed description of the algorithms involved please
refer to the paper listed in the References section.
AMOScmp uses as AMOS messages as both the inputs and the outputs (see
documentation). Two utilities are provided to process these files:
tarchive2amos - a versatile converter from trace archive .seq, .qual,
and .xml information into AMOS formatted data; amos2ace - a converter
from AMOS formatted data to the .ACE assembly format. In addition,
the AMOS::AmosLib Perl module is provided as a tool for users who
prefer to write their own conversion utilities. Please see the
documentation included with the distribution for more information.
AMOScmp is part of the AMOS package (see
http://amos.sourceforge.net/)- a collaborative effort to develop a
modular open-source framework for assembly development.
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annovar
annotate genetic variants detected from diverse genomes
|
|
License: Open Source for non-profit
Debian package not available
|
ANNOVAR is an efficient software tool to utilize update-to-date information
to functionally annotate genetic variants detected from diverse genomes
(including human genome hg18, hg19, as well as mouse, worm, fly, yeast and
many others). Given a list of variants with chromosome, start position, end
position, reference nucleotide and observed nucleotides, ANNOVAR can perform:
1. Gene-based annotation: identify whether SNPs or CNVs cause protein coding
changes and the amino acids that are affected. Users can flexibly use RefSeq
genes, UCSC genes, ENSEMBL genes, GENCODE genes, or many other gene definition
systems.
2. Region-based annotations: identify variants in specific genomic regions,
for example, conserved regions among 44 species, predicted transcription
factor binding sites, segmental duplication regions, GWAS hits, database
of genomic variants, DNAse I hypersensitivity sites, ENCODE
H3K4Me1/H3K4Me3/H3K27Ac/CTCF sites, ChIP-Seq peaks, RNA-Seq peaks, or many
other annotations on genomic intervals.
3. Filter-based annotation: identify variants that are reported in dbSNP,
or identify the subset of common SNPs (MAF>1%) in the 1000 Genome Project,
or identify subset of non-synonymous SNPs with SIFT score>0.05, or many
other annotations on specific mutations.
4. Other functionalities: Retrieve the nucleotide sequence in any
user-specific genomic positions in batch, identify a candidate gene list
for Mendelian diseases from exome data, identify a list of SNPs from
1000 Genomes that are in strong LD with a GWAS hit, and many other
creative utilities.
In a modern desktop computer (3GHz Intel Xeon CPU, 8Gb memory), for
4.7 million variants, ANNOVAR requires ~4 minutes to perform
gene-based functional annotation, or ~15 minutes to perform stepwise
"variants reduction" procedure, making it practical to handle hundreds
of human genomes in a day.
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arachne
toolkit for Whole Genome Shotgun Assembly
|
|
License: free
Debian package not available
|
Arachne is a toolkit developed for Whole Genome Shotgun Assembly.
Arachne consists of a comprehensive set of modules, including a central
pipeline (Assemblez) that can be run on almost any genome to produce a
draft assembly. Arachne's mandate explicitly includes accommodating
difficult genomes with complications such as extreme size, repeats, and
high polymorphism rates. In order to construct a reasonably
well-connected assembly from such tricky genomes, Arachne provides
further tools that can be used after the main module pipeline.
The Arachne code package has been under continuous development since
2000. It began with the classic "overlap-layout-consensus" paradigm and
has since developed into a vast collection of tools, implemented in
numerous modules, to analyze, visualize and manipulate assemblies. New
and improved algorithms are becoming available on a regular basis.
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asap
organize the data associated with a genome
|
|
License: GPL
Debian package not available
|
Developments in genome-wide approaches to biological research have
yielded greatly increased quantities of data, necessitating the cooperation
of communities of scientists focusing on shared sets of data. ASAP
leverages the internet and database technologies to meet these needs.
ASAP is designed to organize the data associated with a genome from the
early stages of sequence annotation through genetic and biochemical
characterization, providing a vehicle for ongoing updates of the annotation
and a repository for genome-scale experimental data. Development was
motivated by the need to more directly involve a greater community of
researchers, with their collective expertise, in keeping the genome
annotation current and to provide a synergistic link between up-to-date
annotation and functional genomic data. The system is continually under
development at the Genome Evolution Lab with the stable, in-use, publicly
available University of Wisconsin installation updated regularly.
Software development on ASAP began in early 2002, and ASAP has been
continually improved up until the present day. A longstanding goal of
the ASAP project was to make the source code of ASAP available so that
other installations of ASAP could be implemented. As future ASAP
installations come to pass, ASAP will be further extended to be
inter-operable between sites.
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bambus
hierarchical approach to building contig scaffolds
|
|
License: Artistic
Debian package not available
|
BAMBUS is the first publicly available scaffolding program. It orders
and orients contigs into scaffolds based on various types of linking
information. Additionally, BAMBUS allows the users to build scaffolds
in a hierarchical fashion by prioritizing the order in which links
are used. For more information please check out the online
documentation.
Note that currently Bambus is undergoing a transition in order to be
integrated with the AMOS package (see http://amos.sourceforge.net/)
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cactus
|
|
License: GPL
Debian package not available
|
Cactus is an open source problem solving environment designed for scientists
and engineers. Its modular structure easily enables parallel computation
across different architectures and collaborative code development between
different groups.
Cactus provides easy access to many cutting edge software technologies being
developed in the academic research community, including the Globus
Metacomputing Toolkit, HDF5 parallel file I/O, the PETSc scientific library,
adaptive mesh refinement, web interfaces, and advanced visualization tools.
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cdna-db
quality-control checking of finished cDNA clone sequences
|
|
License: Artistic
Debian package not available
|
cdna_db is a software system designed for quality-control checking of
finished cDNA clone sequences, and their computational analysis. The
combination of a relational db (MySQL) schema, and an
object-orientated perl API make it easy to implement high-level
analyses of these transcript sequences.
The cdna_db can store cDNA clone sequences, and ESTs and
consensus/contig sequences also derived from these clones. These are
then used by the system to check cDNA clone sequence identity etc
(see deneral_doc.txt). For each clone multiple DNA sequence versions
can be stored, if for instance, the finished DNA sequence is revised
as part of the sequencing process.
A blast pipeline is implemented together with a job control system
(with LSF underlying) so that multiple CPUs can be used in parallel
to carry out the blasts of large datasets. The searches can be made
incremental, so as more cDNA sequences are added to the databank,
just the new clones are blasted.
Utility scripts are provided to delete previous search results, and
dump cDNA clones sequences (such as those that passed the QC
checking) from the cdna_db.
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cmap
view comparisons of genetic and physical maps
|
|
License: Not specified
Debian package not available
|
CMap is a web-based tool that allows users to view comparisons of genetic and
physical maps. The package also includes tools for curating map data.
|
contralign
parameter learning framework for protein pairwise sequence alignment
|
|
License: Public Domain
Debian package not available
|
CONTRAlign is an extensible and fully automatic parameter learning
framework for protein pairwise sequence alignment based on pair
conditional random fields. The CONTRAlign framework enables the
development of feature-rich alignment models which generalize well to
previously unseen sequences and avoid overfitting by controlling model
complexity through regularization.
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copycat
fast access to cophylogenetic analyses
|
|
License: Use of the program is free for academic purposes at an academic institute. For all other uses, please contact the authors.
Debian package not available
|
CopyCat provides an easy and fast access to cophylogenetic analyses.
It incorporates a wrapper for the program ParaFit, which conducts a
statistical test for the presence of congruence between host and
parasite phylogenies. CopyCat offers various features, such as the
creation of customized host-parasite association data and the
computation of phylogenetic host/parasite trees based on the NCBI taxonomy.
|
e-hive
distributed processing system based on 'autonomous agents'
|
|
License: Not specified
Debian package not available
|
This is a distributed processing system based on 'autonomous agents' and
Hive behavioural structure of Honey Bees . It implements all functionality
of both data-flow graphs and block-branch diagrams which should allow it
to codify any program, algorithm, or parallel processing job control system.
It is not bound to any processing 'farm' system and can be adapted to any GRID.
|
exalt
phylogenetic generalized hidden Markov model for predicting alternatively spliced exons
|
|
License: Artistic
Debian package not available
|
ExAlt is a software program designed to predict alternatively spliced
overlapping exons in genomic sequence. The program works in several
ways depending on the available input. ExAlt can use information of
existing gene structure as well as sequence conservation to improve
the precision of it's predictions. ExAlt can also make predictions
when only a single genomic sequence is available. ExAlt has been
extensively tested on Drosophila melanogaster, but can be adapted to
run on other species.
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excavator
gene expression data clustering
|
|
License: GPL
Debian package not available
Language: Java
|
Excavator is a program for gene expression data clustering. It uses a set of unique
clustering algorithms developed by the Computational Systems Biology Lab (CSBL) at
the University of Georgia. Excavator represents data internally as a minimum spanning
tree and outputs results to the user through the use of a micro-array data window,
graphs, and a dendrogram viewer.
Features
- partitioning gene expressions profiles using multiple methods of clustering and
definitions of distance between profiles.
- automatic selection of the most plausible number of clusters in a data set
- three different ways of viewing data: Micro-array, Gene Expression, and Dendrogram.
As well as graphing individual genes from each cluster independently.
- identification of genes with expression profiles similar to specified seed genes
- cluster identification from a noisy background
- numerical comparison between different clustering results of the same data set
- runnable on command line as well as through a Java GUI
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figaro
novel vector trimming software
|
|
License: Artistic
Debian package not available
|
Figaro is a software tool for identifying and removing the vector
from raw DNA sequence data without prior knowledge of the vector
sequence. By statistically modeling short oligonucleotide
frequencies within a set of reads, Figaro is able to determine which
DNA words are most likely associated with vector sequence. For a
description of Figaro's algorithms please see our paper. Figaro is
part of the AMOS suite.
|
forge
genome assembler for mixed read types
|
|
License: Apache 2.0
Debian package not available
|
Forge Genome Assembler is a parallel, MPI based genome assembler for
mixed read types.
Forge is a classic "Overlap layout consensus" genome assembler written
by Darren Platt and Dirk Evers. Implemented in C++ and using the
parallel MPI library, it runs on one or more machines in a network and
can scale to very large numbers of reads provided there is enough
collective memory on the machines used. It generates a full consensus
alignment of all reads, can handle mixtures of sanger, 454 and illumina
reads. There is some support for solid color space and it includes built
in tools for vector trimming and contamination screening.
Forge and was originally developed at Exelixis and they have kindly
agreed to place the software which underwent much subsequent development
outside Exelixis, into the public domain. Forge works with most of the
common MPI implementations.
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gbrowse-syn
|
|
License: Not specified
Debian package not available
|
GBrowse_syn, or the Generic Synteny Browser, is a GBrowse-based synteny
browser designed to display multiple genomes, with a central reference
species compared to two or more additional species. It can be used to
view multiple sequence alignment data, synteny or co-linearity data
from other sources against genome annotations provided by GBrowse.
GBrowse_syn is included with the standard GBrowse package (version 1.69 and
later). Working examples can be seen at TAIR and WormBase.
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genemark
family of gene prediction programs
|
|
License: Academic License Agreement
Debian package not available
|
A family of gene prediction programs developed at Georgia Institute of
Technology, Atlanta, Georgia, USA.
|
genesplicer
computational method for splice site prediction
|
|
License: Artistic
Debian package not available
|
A fast, flexible system for detecting splice sites in the genomic DNA
of various eukaryotes. The system has been trained and tested
successfully on Plasmodium falciparum (malaria), Arabidopsis
thaliana, human, Drosophila, and rice . Training data sets for human
and Arabidopsis thaliana are included. Use the GeneSplicer Web
Interface to run GeneSplicer directly, or see below for instructions
on downloading the complete system including source code.
There is no independent program to train GeneSplicer, but there is a
way to obtain the necessary files by using the training procedure of
GlimmerHMM.
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genetrack
genomic data storage and visualization framework
|
|
License: MIT
Debian package not available
|
GeneTrack is a high performance bioinformatics data storage and analysis
system designed to store genome wide information. It is currently used to
analyze data obtained via high-throughput rapid sequencing platforms such as
the 454 and Solexa as well as tiling array data based on various platforms.
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genezilla
|
|
License: Artistic
Debian package not available
Language: C++
|
GeneZilla is a state-of-the-art program for computational prediction
of protein-coding genes in eukaryotic DNA, and is based on the
Generalized Hidden Markov Model (GHMM) framework, similar to GENSCAN
and GENIE. It is highly reconfigurable and includes software for
retraining by the end-user. It is written in highly optimized C++ and
runs under most UNIX/Linux platforms. The run time and memory
requirements are linear in the sequence length, and are in general
much better than those of competing systems, due to GeneZilla's novel
decoding algorithm. Graph-theoretic representations of the high
scoring open reading frames are provided, allowing for exploration of
sub-optimal gene models. It utilizes Interpolated Markov Models
(IMMs), Maximal Dependence Decomposition (MDD), and includes states
for signal peptides, branch points, TATA boxes, CAP sites, and will
soon model CpG islands as well.
GeneZilla is an open-source project hosted at bioinformatics.org and
currently consists of ~20,000 lines of code. GeneZilla evolved out
of the ab initio eukaryotic gene finder TIGRscan, which was developed
at The Institute for Genomic Research over a 3-year period under NIH
grants R01-LM06845 and R01-LM007938, and which served as the basis
for the comparative gene finder TWAIN.
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genographer
read data and reconstruct them into a gel image
|
|
License: GPL
Debian package not available
|
This program will read in data from an ABI 3700, 3100, 377 or 373,
CEQ 2000 or SCF and reconstruct them into a gel image which is
straightened and sized. Bins can be defined easily and viewed as
thumbnails, which allows for a fairly quick and easy way of scoring a gel.
The program is written in Java and uses the Java 1.3 API. Therefore,
it should run on any machine that can run java.
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glimmerhmm
Eukaryotic Gene-Finding System
|
|
License: Artistic
Debian package not available
|
GlimmerHMM is a new gene finder based on a Generalized Hidden Markov
Model (GHMM). Although the gene finder conforms to the overall
mathematical framework of a GHMM, additionally it incorporates splice
site models adapted from the GeneSplicer program and a decision tree
adapted from GlimmerM. It also utilizes Interpolated Markov Models
for the coding and noncoding models . Currently, GlimmerHMM's GHMM
structure includes introns of each phase, intergenic regions, and
four types of exons (initial, internal, final, and single). A basic
user manual can be consulted here.
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gmv
comparative genome browser for Murasaki
|
|
License: GPL
Debian package not available
|
GMV is a comparative genome browser for Murasaki. GMV visualizes
anchors from Murasaki, annotation data from GenBank files, and
expression / prediction score from GFF files.
|
jigsaw
gene prediction using multiple sources of evidence
|
|
License: Artistic
Debian package not available
|
JIGSAW is a program designed to use the output from gene finders,
splice site prediction programs and sequence alignments to predict
gene models. The program provides an automated way to take advantage
of the many succsessful methods for computational gene prediction and
can provide substantial improvements in accuracy over an individual
gene prediction program.
JIGSAW is available for all species. It is tested on Human, Rice
(Oryza sativa), Arabidopsis thaliana , Brugia malayi, Cryptococcus
neoformans, Entamoeba histolytica, Theileria parva, Aspergillus
fumigatus, Plasmodium falciparum and Plasmodium yoelii.
The linear combiner option is now available in the current JIGSAW
software distribution. This allows JIGSAW to be run without the use
of training data. A weight is assigned to each evidence source, and
gene predictions are based on a weighted voting scheme, yielding the
best 'consensus' predictions.
Predictions are now available for the ENCODE regions in Human and
viewable as custom tracks in the UCSC Human Genome
Browser. Predictions available for the Human genome and viewable as
custom tracks in the UCSC Human Genome Browser
|
maker2
annotate genomes and create genome databases
|
|
License: GPL / Artistic
Debian package not available
|
MAKER is a portable and easily configurable genome annotation pipeline.
It's purpose is to allow smaller eukaryotic and prokaryotic genome
projects to independently annotate their genomes and to create genome
databases. MAKER identifies repeats, aligns ESTs and proteins to a
genome, produces ab-initio gene predictions and automatically
synthesizes these data into gene annotations having evidence-based
quality values. MAKER is also easily trainable: outputs of preliminary
runs can be used to automatically retrain its gene prediction algorithm,
producing higher quality gene-models on seusequent runs. MAKER's inputs
are minimal and its ouputs can be directly loaded into a GMOD database.
They can also be viewed in the Apollo genome browser; this feature of
MAKER provides an easy means to annotate, view and edit individual
contigs and BACs without the overhead of a database. MAKER should prove
especially useful for emerging model organism projects with minimal
bioinformatics expertise and computer resources
|
metarep
JCVI Metagenomics Reports
|
|
License: MIT
Debian package not available
|
JCVI Metagenomics Reports (METAREP) is a new open source tool for
high-performance comparative metagenomics. It provides a suite of web
based tools to help scientists to view, query, browse and compare
metagenomics annotation data derived from ORFs called on metagenomics
reads.
METAREP supports browsing of functional and taxonomic assignments.
Users can either specify fields, or logical combinations of fields to
flexibly filter datasets on the fly. Users can compare multiple datasets
at various functional and taxonomic levels applying statistical tests as
well as hierarchical clustering, multidimensional scaling and heatmaps.
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minimus
AMOS lightweight assembler
|
|
License: Artistic
Debian package not available
|
minimus is an assembly pipeline designed specifically for small
data-sets, such as the set of reads covering a specific gene. Note
that the code will work for larger assemblies (we have used it to
assemble bacterial genomes), however, due to its stringency, the
resulting assembly will be highly fragmented. For large and/or
complex assemblies the execution of Minimus should be followed by
additional processing steps, such as scaffolding.
minimus follows the Overlap-Layout-Consensus paradigm and consists of three main modules:
- overlapper - computes the overlaps between the reads using a
modified version of the Smith-Waterman local alignment algorithm
- tigger - uses the read overlaps to generate the layouts of reads
representing individual contigs
- make-consensus - refines the layouts produced by the tigger to
generate accurate multiple alignments within the reads
minimus uses as AMOS messages as both the inputs and the outputs (see
documentation). Two utilities are provided to process these files:
tarchive2amos - a versatile converter from trace archive .seq, .qual,
and .xml information into AMOS formatted data; amos2ace - a converter
from AMOS formatted data to the .ACE assembly format. In addition,
the AMOS::AmosLib Perl module is provided as a tool for users who
prefer to write their own conversion utilities. Please see the
documentation included with the distribution for more information.
minimus is part of the AMOS package - a collaborative effort to
develop a modular open-source framework for assembly development.
|
mummergpu
High-throughput sequence alignment using Graphics Processing Units
|
|
License: Artistic
Debian package not available
|
The recent availability of new, less expensive high-throughput DNA
sequencing technologies has yielded a dramatic increase in the volume
of sequence data that must be analyzed. These data are being
generated for several purposes, including genotyping, genome
resequencing, metagenomics, and de novo genome assembly
projects. Sequence alignment programs such as MUMmer have proven
essential for analysis of these data, but researchers will need ever
faster, high-throughput alignment tools running on inexpensive
hardware to keep up with new sequence technologies.
MUMmerGPU is a low cost, ultra-fast sequence alignment program
designed to handle the increasing volume of data produced by new,
high-throughput sequencing technologies. MUMmerGPU is a GPGPU drop-in
replacement for MUMmer, using the GPUs in common workstations to
simultaneously align multiple query sequences against a single
reference sequence stored as a suffix tree. By processing the queries
in parallel on the highly parallel graphics card, MUMmerGPU achieves
more than a 10-fold speedup over a serial CPU version of the sequence
alignment kernel, and outperforms MUMmer on a high end CPU by
3.5-fold in total application time when aligning reads from recent
sequencing projects using Solexa/Illumina, 454, and Sanger sequencing
technologies.
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obo-edit
editor for biological ontologies
|
|
License: Artistic
Debian package not available
|
(Open Biological Ontologies) Obo-Edit supports the formal representation
of biological entities and the specification of is-a (specialisation)
and part-of relations. Amongst the databases cureated by this tool
is the GeneOntology.
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operondb
detect and analyze conserved gene pairs
|
|
License: to be clarified
Debian package not available
|
Comparison of complete microbial genomes reveals a large number of
conserved gene clusters - sets of genes that have the same order in
two or more different genomes. Such gene clusters often, but not
always represent a co-transcribed unit, or operon. A method was
developed to detect and analyze conserved gene pairs - pairs of genes
that are located close on the same DNA strand in two or more
bacterial genomes. For each conserved gene pair, an estimate of
probability is calculated that the genes belong to the same
operon. The algorithm takes into account several alternative
possibilities. One is that functionally unrelated genes may have the
same order due simply because they were adjacent in a common
ancestor. Other possibilities are that genes may be adjacent in two
genomes by chance alone, or due to horizontal transfer of the gene
pair.
The method is modified from the one described in: Maria D. Ermolaeva,
Owen White and Steven L. Salzberg. Prediction of Operons in Microbial
Genomes. Nucleic Acids Research, 29, 1216-1221, (2001)
OperonDB was supported by the NIH under grant R01-LM007938 and by the
NSF under grant DBI-0234704.
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phagefinder
heuristic computer program to identify prophage regions within bacterial genomes
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License: GPL
Debian package not available
Language: Perl
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It uses tab-delimited results from NCBI BLASTALL or WU BLASTP 2.0 searches against a
collection of bacteriophage protein sequences and results from HMMSEARCH analysis of
441 phage-specific HMMs to locate prophage regions. By using FASTA33, MUMMER or BLASTN,
it can find potential attachment (att) sites of the phage region(s). Data from tRNAscan-SE
and Aragorn are used to determine whether a tRNA or tmRNA served as the putative target
for integration. Additionally, by looking for the presence or absence of specific proteins
using specific HMM models, Phage_Finder can predict whether the region is most likely
prophage and which type (Mu, P2, or retron R73), an integrated element, a plasmid, or a
degenerate phage region.
The goal of this project is to provide an open-sourced, standardized and automated system
to identify and classify prophages within prokaryotic genomes. It is hoped that this package
will facilitate future studies on the biology and evolution of these prophages by providing
a level of microbial genome annotation that was previously void.
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phpphylotree
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License: GPL
Debian package not available
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PhpPhylotree is a web application that is able to draw phylogenetic trees.
It produces an SVG (Scalable Vector Graphic) file from phylip/newick tree files.
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phylographer
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License: GPL
Debian package not available
Language: Tcl/Tk
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PhyloGrapher is a program designed to visualize and study evolutionary
relationships within families of homologous genes or proteins
(elements). PhyloGrapher is a drawing tool that generates custom graphs
for a given set of elements. In general, it is possible to use
PhyloGrapher to visualize any type of relations between elements.
Used in conjunction with tcl_blast_parser, PhyloGrapher can represent
the results of a BLAST search as a graph.
PhyloGrapher and tcl_blast_parser are useful tools to analyse BLAST
biological sequence alignment reports (BLAST is provided by Debian's
blast2 package).
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pyrophosphate-tools
for assembling and searching pyrophosphate sequence data
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License: not specified
Debian package not available
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Simple tools for assembling and searching high-density picolitre
pyrophosphate sequence data.
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rose
Region-Of-Synteny Extractor
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License: Open Source
Debian package not available
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ROSE is a program which identifies regions between two genomes which
are likely to contain orthologous genes. The two genomes are given as
two multi fasta files of DNA sequences. The PROmer program from the
MUMmer package needs to be run first between the two genomes, and the
resulting delta file is then input to ROSE. If a previous annotation
is available for one or both genomes, then the coordinates of the
annotated genes from a genome can be optionally given as input in a
gff file. The gene coordinates will be used to guide the length of
the regions produced by ROSE. By default, when finding a region of
consistent alignments, ROSE will add a user-defined margin (1000 bp
by default) on either side of that region. When a predicted gene
overlaps an alignment we use the gene prediction to extend the
boundaries of the output region.
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treebuilder3d
viewer of SAGE and other types of gene expression data
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License: GPL
Debian package not available
Language: Java
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TreeBuilder3D is an interactive viewer that allows organization of SAGE and other
types of gene expression data such as microarrays into hierarchical dendrograms,
or phenetic networks (the term 'phenetic' used as the analysis relies on principals,
used in phylogenetic analysis by system biology). Might be used as a visual aid when
analyzing differences in expression profiles of SAGE libraries, serves as an
alternative to Venn diagrams.
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tripal
collection of Drupal modules for genomic research
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License: GPL ( as Drupal a derivative )
Debian package not available
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Tripal is a collection of open-source freely available Drupal modules under
development at CUGI and a member of the GMOD family of tools. Tripal serve
as a web interface for the GMOD Chado database. Tripal intially started as
a web front-end for the Marine Genomics Project (MG.org). Work on the
interface is currently ongoing for the MG.org project as well as the
Fagaceae Genomics Web, and other CUGI projects. Tripal is currently being
implemented for the new Cacao Genome Database, and Citrus Genome Database
and will be used for the Genome Database for Rosaceae. These latter three
databases are projects of the Main Bioinformatics Laboratory at Washington
State University
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twain
syntenic genefinder employing a Generalized Pair Hidden Markov Model
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License: Open Source
Debian package not available
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TWAIN is a new syntenic genefinder which employs a Generalized Pair
Hidden Markov Model (GPHMM) to predict genes in two closely related
eukaryotic genomes simultaneously. It utilizes the MUMmer package to
perform approximate alignment before applying a GPHMM based on an
enhanced version of the TigrScan gene finder. TWAIN was written by
Bill Majoros and Mihaela Pertea while at The Institute for Genomic
Research (TIGR).
TWAIN consists of two components: (1) ROSE, the Region Of Synteny
Extractor, which identifies contiguous regions likely to contain one
or more syntenic genes, and (2) OASIS, a generalized pair hidden
Markov model (GPHMM) for predicting genes in the regions identified
by ROSE. The system utilizes approximate alignments constructed by
the PROmer and NUCmer programs in the MUMmer package to assess
approximate alignment scores efficiently. More detailed information
on the architecture of this system will be made available soon.
Slides from a talk at Computational Genomics 2004 are now available.
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uniprime
workflow-based platform for universal primer design
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License: GPL-3+
Debian package not available
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UniPrime automatically designs large sets of universal primers by simply
inputting a GeneID reference. It automatically retrieves and aligns
orthologous sequences from GenBank, identifies regions of conservation within
the alignment and generates suitable primers that can amplify variable genomic
regions. UniPrime differs from previous automatic primer design programs in
that all steps of primer design are automated, saved and are phylogenetically
limited. We have experimentally verified the efficiency and success of this
program. UniPrime is an experimentally validated, fully automated program that
generates successful cross-species primers that take into account the
biological aspects of the PCR.
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x-tandem-pipeline
peptide/protein identification from MS/MS mass spectra
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License: GPL
Debian package not available
Language: Java
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X!Tandem is an open-source software performing peptide/protein
identification from MS/MS mass spectra. X!Tandem is fast and accurate,
but the Global Proteome Machine (GPM) is relatively limited regarding
the processing of identification results. X!Tandem pipeline is an
alternative to the installation of the GPM on local servers. X!Tandem
pipeline performs database searching and matching on a list of MS/MS
runs in one shot, using a list of easily user selected paramaters and
databases. X!Tandem pipeline also performs filtering of data according
to statistical values at peptide and protein levels. The results are
stored into TSV (Tab Separated Values) files. Moreover, redundancy of
protein databases are fully filtered as follows :
- proteins identified without specific peptides compared to others are
eliminated;
- proteins identified with the same pool of peptides are assembled;
- proteins are grouped by function (identified with at least one common
peptide), and the specific peptides for each sub-group of proteins are
indicated.
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