Summary
Cloud
Debian Med bioinformatics applications usable in cloud computing
This metapackage will install Debian packages related to molecular biology,
structural biology and bioinformatics for use in life sciences, that do not
depend on graphical toolkits and therefore can fit on system images for use
in cloud computing clusters, where space can be limited.
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 Cloud packages
Official Debian packages with high relevance
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 |
stretch | 2.0.2-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch-backports | 2.1.5-7~bpo9+1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.1.5-7 | amd64,arm64,armhf,i386 |
jessie | 1.5.2-1 (non-free) | amd64 |
sid | 2.3.10-1 | amd64,arm64,mips64el,ppc64el,riscv64 |
trixie | 2.3.10-1 | amd64,arm64,mips64el,ppc64el,riscv64 |
bookworm | 2.3.5+dfsg-2 | amd64,arm64,mips64el,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 |
stretch | 4.9.39+dfsg.02-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 4.9.39+dfsg.01-5 | amd64,armel,armhf,i386 |
sid | 4.9.39+dfsg.02-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 4.9.39+dfsg.02-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 4.9.39+dfsg.02-5 | amd64,arm64,armel,armhf,i386,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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aevol
digital genetics model to run Evolution Experiments in silico
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Versions of package aevol |
Release | Version | Architectures |
sid | 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 |
buster | 5.0-2 | amd64,arm64,armhf,i386 |
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 |
trixie | 5.0+ds-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,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 |
jessie | 1.7-3 | all |
sid | 1.7-10 | all |
trixie | 1.7-10 | all |
bookworm | 1.7-10 | all |
bullseye | 1.7-8 | all |
buster | 1.7-7 | all |
stretch | 1.7-5 | 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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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 |
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 |
stretch | 1.3.1-4 | amd64,arm64,armel,armhf,i386,mips,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 |
sid | 2.2+git20080214.600fc29+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,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 |
stretch | 2.2-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,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 |
trixie | 1.29-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.29-8 | amd64,arm64,armhf,i386 |
stretch | 1.29-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.29-2 | amd64,armel,armhf,i386 |
bullseye | 1.29-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.29-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.29-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,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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anfo
Short Read Aligner/Mapper from MPG
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Versions of package anfo |
Release | Version | Architectures |
bullseye | 0.98-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.98-7 | amd64,arm64,armhf,i386 |
stretch | 0.98-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0.98-4 | amd64,armel,armhf,i386 |
sid | 0.98-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x |
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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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aragorn
tRNA and tmRNA detection in nucleotide sequences
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Versions of package aragorn |
Release | Version | Architectures |
bookworm | 1.2.38-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.2.38-2 | amd64,arm64,armhf,i386 |
bullseye | 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 |
jessie | 1.2.36-4 | amd64,armel,armhf,i386 |
sid | 1.2.41-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.2.41-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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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 |
stretch | 1.0-3 | all |
jessie | 1.0-1 | amd64,armel,armhf,i386 |
sid | 1.0-6 | all |
trixie | 1.0-6 | all |
bookworm | 1.0-5 | all |
bullseye | 1.0-5 | all |
buster | 1.0-4 | 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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autodock
analysis of ligand binding to protein structure
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Versions of package autodock |
Release | Version | Architectures |
stretch | 4.2.6-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 4.2.6-2 | amd64,armel,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 |
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 |
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
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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 |
trixie | 1.2.5-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.1.2-3 | amd64,armel,armhf,i386 |
stretch | 1.1.2-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.1.2-5 | amd64,arm64,armhf,i386 |
bullseye | 1.1.2-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.2.3-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,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 |
stretch | 4.2.6-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 4.2.6-6 | amd64,arm64,armhf,i386 |
bullseye | 4.2.6-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 4.2.6-2 | amd64,armel,armhf,i386 |
trixie | 4.2.6-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,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 |
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
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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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bamtools
toolkit for manipulating BAM (genome alignment) files
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Versions of package bamtools |
Release | Version | Architectures |
trixie | 2.5.2+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.5.2+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 2.4.1+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.5.1+dfsg-3 | amd64,arm64,armhf,i386 |
jessie | 2.3.0+dfsg-2 | amd64,armel,armhf,i386 |
bookworm | 2.5.2+dfsg-4 | amd64,arm64,armel,armhf,i386,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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bedtools
suite of utilities for comparing genomic features
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Versions of package bedtools |
Release | Version | Architectures |
stretch | 2.26.0+dfsg-3 | amd64,arm64,armel,i386,mips64el,mipsel,ppc64el |
bookworm | 2.30.0+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.30.0+dfsg-1 | 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 |
buster | 2.27.1+dfsg-4 | amd64,arm64,armhf |
jessie | 2.21.0-1 | amd64,armhf,i386 |
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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bioperl
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Versions of package bioperl |
Release | Version | Architectures |
stretch | 1.7.1-2 | all |
jessie | 1.6.924-1 | all |
trixie | 1.7.8-1 | all |
bullseye | 1.7.7-2 | all |
buster | 1.7.2-3 | all |
bookworm | 1.7.8-1 | all |
sid | 1.7.8-1 | all |
Debtags of package bioperl: |
devel | lang:perl, library |
field | biology, biology:bioinformatics |
role | devel-lib, shared-lib |
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License: DFSG free
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Bioperl 项目致力于将各种生物信息学的处理工具收集起来,汇集成一系列符合 CPAN
标准格式、有良好文档支持又免费可用的 Perl 模块。现在它不仅已被社区广泛接
受,还用于许多高通量项目,如 Ensembl。
本包包含的某些可执行文件需要推荐安装的软件包才能运行。如需了解详细的情况,
包括各个单独 Perl 模块的信息,请查阅 README.Debian 文件。
建议安装的软件包提供增强的 man 手册页。
Please cite:
Jason E Stajich, David Block, Kris Boulez, Steven E Brenner, Stephen A Chervitz, Chris Dagdigian, Georg Fuellen, James G R Gilbert, Ian Korf, Hilmar Lapp, Heikki Lehvaslaiho, Chad Matsalla, Chris J Mungall, Brian I Osborne, Matthew R Pocock, Peter Schattner, Martin Senger, Lincoln D Stein, Elia Stupka, Mark D Wilkinson and Ewan Birney:
The Bioperl toolkit: Perl modules for the life sciences.
(PubMed,eprint)
Genome Res.
12(10):1611-1618
(2002)
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bioperl-run
BioPerl wrappers: scripts
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Versions of package bioperl-run |
Release | Version | Architectures |
stretch | 1.7.1-3 | all |
jessie | 1.6.9-2 | all |
trixie | 1.7.3-13 | all |
sid | 1.7.3-13 | all |
buster | 1.7.2-4 | all |
bullseye | 1.7.3-6 | all |
bookworm | 1.7.3-9 | all |
Debtags of package bioperl-run: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
|
License: DFSG free
|
Contains scripts from the BioPerl-Run package. This package will also install
all wrappable applications packaged in Debian. The ones that are not Free are
"Suggested" by this package.
|
|
biosquid
utilities for biological sequence analysis
|
Versions of package biosquid |
Release | Version | Architectures |
sid | 1.9g+cvs20050121-15.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.9g+cvs20050121-12 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.9g+cvs20050121-12 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.9g+cvs20050121-7 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch-backports | 1.9g+cvs20050121-11~bpo9+1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.9g+cvs20050121-11 | amd64,arm64,armhf,i386 |
jessie | 1.9g+cvs20050121-4 | amd64,armel,armhf,i386 |
trixie | 1.9g+cvs20050121-15.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package biosquid: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | comparing, converting, editing |
|
License: DFSG free
|
SQUID is a library of C code functions for sequence analysis. It also
includes a number of small utility programs to convert, show statistics,
manipulate and do other functions on sequence files.
The original name of the package is "squid", but since there is already
a squid on the archive (a proxy cache), it was renamed to "biosquid".
This package contains some tools to demonstrate the features of the
SQUID library.
|
|
blast2
transitional dummy package to ncbi-blast+-legacy
|
Versions of package blast2 |
Release | Version | Architectures |
buster | 2.8.1-1+deb10u1 | all |
stretch | 2.6.0-1 | all |
jessie | 2.2.26.20120620-8 | amd64,armel,armhf,i386 |
Debtags of package blast2: |
biology | nuceleic-acids, peptidic |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
science | calculation |
scope | utility |
use | searching |
works-with | biological-sequence |
|
License: DFSG free
|
This is a transitional dummy package for ncbi-blast+-legacy.
It can safely be removed.
The package is enhanced by the following packages:
mcl
|
|
bowtie
Ultrafast memory-efficient short read aligner
|
Versions of package bowtie |
Release | Version | Architectures |
jessie | 1.1.1-2 | amd64 |
buster | 1.2.2+dfsg-4 | amd64,arm64 |
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 |
bookworm | 1.3.1-1 | amd64,arm64,mips64el,ppc64el,s390x |
bullseye | 1.3.0+dfsg1-1 | 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).
|
|
bowtie2
ultrafast memory-efficient short read aligner
|
Versions of package bowtie2 |
Release | Version | Architectures |
trixie | 2.5.4-1 | amd64,arm64,mips64el,ppc64el,riscv64 |
bookworm | 2.5.0-3 | amd64,arm64,mips64el,ppc64el |
jessie | 2.2.4-1 | amd64 |
bullseye | 2.4.2-2 | amd64,arm64,mips64el,ppc64el |
stretch | 2.3.0-2 | amd64 |
sid | 2.5.4-1 | amd64,arm64,mips64el,ppc64el,riscv64 |
buster | 2.3.4.3-1 | amd64 |
|
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
|
|
boxshade
Pretty-printing of multiple sequence alignments
|
Versions of package boxshade |
Release | Version | Architectures |
trixie | 3.3.1-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 3.3.1-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 3.3.1-12 | amd64,arm64,armhf,i386 |
stretch | 3.3.1-10 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 3.3.1-8 | amd64,armel,armhf,i386 |
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 |
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
|
|
bwa
|
Versions of package bwa |
Release | Version | Architectures |
stretch | 0.7.15-2+deb9u1 | amd64 |
bookworm | 0.7.17-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.7.17-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.7.18-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.7.18-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 0.7.10-1 | amd64 |
buster | 0.7.17-3 | amd64 |
stretch-backports | 0.7.17-1~bpo9+1 | 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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cassiopee
index and search tool in genomic sequences
|
Versions of package cassiopee |
Release | Version | Architectures |
stretch | 1.0.5-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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 |
bookworm | 1.0.9-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.0.1+dfsg-3 | amd64,armel,armhf,i386 |
trixie | 1.0.9-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.0.9-2 | amd64,arm64,armhf,i386 |
|
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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cd-hit
suite of programs designed to quickly group sequences
|
Versions of package cd-hit |
Release | Version | Architectures |
buster | 4.6.8-2 | amd64,arm64,armhf,i386 |
sid | 4.8.1-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 4.8.1-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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 |
stretch | 4.6.6-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 4.6.1-2012-08-27-2 | amd64,armel,armhf,i386 |
|
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 |
trixie | 1.00+git20230710.da8f5ba+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 0.99-20100722-5 | amd64,arm64,armhf,i386 |
jessie | 0.99-20100722-1 | amd64,armel,armhf,i386 |
sid | 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 |
stretch | 0.99-20100722-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.00+git20181005.014498c+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
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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circos
plotter for visualizing data
|
Versions of package circos |
Release | Version | Architectures |
bookworm | 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 |
sid | 0.69.9+dfsg-2 | all |
bullseye | 0.69.9+dfsg-2 | all |
trixie | 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 |
trixie | 1.0.9+git20211013.b799afe-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.0.9+git20211013.b799afe-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.9-3 | amd64,arm64,armhf,i386 |
stretch | 1.0.9-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.0.9-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.0.9-1 | amd64,armel,armhf,i386 |
|
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 |
buster | 1.2-9 | amd64,arm64,armhf,i386 |
stretch | 1.2-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.2-3 | amd64,armel,armhf,i386 |
bookworm | 1.2-11 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.2-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.2-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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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clustalo
General-purpose multiple sequence alignment program for proteins
|
Versions of package clustalo |
Release | Version | Architectures |
bookworm | 1.2.4-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.2.1-1 | amd64,armel,armhf,i386 |
stretch | 1.2.4-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.2.4-2 | amd64,arm64,armhf,i386 |
bullseye | 1.2.4-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.2.4-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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
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clustalw
global multiple nucleotide or peptide sequence alignment
|
Versions of package clustalw |
Release | Version | Architectures |
buster | 2.1+lgpl-6 | amd64,arm64,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 |
trixie | 2.1+lgpl-7 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
jessie | 2.1+lgpl-4 | amd64,armel,armhf,i386 |
bookworm | 2.1+lgpl-7 | amd64,arm64,armel,armhf,i386,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
|
|
concavity
predictor of protein ligand binding sites from structure and conservation
|
Versions of package concavity |
Release | Version | Architectures |
buster | 0.1+dfsg.1-4 | amd64,arm64,armhf,i386 |
bullseye | 0.1+dfsg.1-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.1+dfsg.1-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.1+dfsg.1-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 0.1+dfsg.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0.1-2 | amd64,armel,armhf,i386 |
sid | 0.1+dfsg.1-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,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 |
jessie | 20110309.0-3 | all |
sid | 20110309.0-8 | all |
stretch | 20110309.0-5 | all |
buster | 20110309.0-7 | all |
trixie | 20110309.0-8 | all |
bookworm | 20110309.0-8 | all |
bullseye | 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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datamash
statistics tool for command-line interface
|
Versions of package datamash |
Release | Version | Architectures |
bullseye | 1.7-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.4-1 | amd64,arm64,armhf,i386 |
bookworm | 1.7-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.0.6-2 | amd64,armel,armhf,i386 |
trixie | 1.8-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.8-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.0.7-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
|
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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dialign
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Versions of package dialign |
Release | Version | Architectures |
sid | 2.2.1-13 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 2.2.1-7 | amd64,armel,armhf,i386 |
buster | 2.2.1-10 | amd64,arm64,armhf,i386 |
bullseye | 2.2.1-11 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.2.1-11 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.2.1-13 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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 |
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License: DFSG free
|
DIALIGN2 是一个进行蛋白质或 DNA 序列多重比对
的命令行工具。它从序列相似段
的无空位(gap free)对构建比对。用于比对的记分
系统是 DIALIGN 与其他全局或局部比对方法
的基本区别。注意:DIALIGN 不使用任何类型的间隔
惩罚(gap penalty)。
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dialign-tx
Segment-based multiple sequence alignment
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Versions of package dialign-tx |
Release | Version | Architectures |
trixie | 1.0.2-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.0.2-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.0.2-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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 |
jessie | 1.0.2-7 | amd64,armel,armhf,i386 |
Debtags of package dialign-tx: |
field | biology, biology:bioinformatics |
role | program |
scope | utility |
use | comparing |
works-with-format | plaintext |
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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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discosnp
discovering Single Nucleotide Polymorphism from raw set(s) of reads
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Versions of package discosnp |
Release | Version | Architectures |
jessie | 1.2.5-1 | amd64,armel,armhf,i386 |
stretch | 1.2.6-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.3.0-2 | amd64,arm64,i386 |
bullseye | 4.4.4-1 | amd64,arm64,i386,mips64el,ppc64el,s390x |
sid | 2.6.2-4 | amd64,arm64,mips64el,ppc64el,riscv64 |
trixie | 2.6.2-4 | amd64,arm64,mips64el,ppc64el,riscv64 |
bookworm | 2.6.2-2 | amd64,arm64,mips64el,ppc64el |
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License: DFSG free
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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
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Versions of package disulfinder |
Release | Version | Architectures |
jessie | 1.2.11-4 | amd64,armel,armhf,i386 |
stretch | 1.2.11-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.2.11-8 | amd64,arm64,armhf,i386 |
bullseye | 1.2.11-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.2.11-12 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.2.11-12 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.2.11-12 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package disulfinder: |
role | program |
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License: DFSG free
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'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
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Versions of package dnaclust |
Release | Version | Architectures |
trixie | 3-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 3-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 3-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 3-6 | amd64,arm64,armhf,i386 |
stretch | 3-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 3-2 | amd64,armel,armhf,i386 |
sid | 3-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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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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dssp
protein secondary structure assignment based on 3D structure
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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 |
stretch | 2.2.1-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 4.0.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 3.0.0-3 | amd64,arm64,armhf,i386 |
bookworm | 4.2.2-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 2.2.1-2 | amd64,armel,armhf,i386 |
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License: DFSG free
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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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embassy-domainatrix
Extra EMBOSS commands to handle domain classification file
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Versions of package embassy-domainatrix |
Release | Version | Architectures |
bullseye | 0.1.660-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 0.1.650-1 | amd64,armel,armhf,i386 |
bookworm | 0.1.660-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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 |
buster | 0.1.660-3 | amd64,arm64,armhf,i386 |
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 |
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License: DFSG free
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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
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Versions of package embassy-domalign |
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 |
sid | 0.1.660-5 | amd64,arm64,mips64el,ppc64el,riscv64 |
bookworm | 0.1.660-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.1.660-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.1.660-3 | amd64,arm64,armhf,i386 |
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 |
trixie | 0.1.660-4 | amd64,arm64,mips64el,ppc64el,riscv64 |
bullseye | 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 |
jessie | 0.1.650-1 | amd64,armel,armhf,i386 |
buster | 0.1.660-3 | amd64,arm64,armhf,i386 |
sid | 0.1.660-4 | amd64,arm64,mips64el,ppc64el,riscv64 |
bookworm | 0.1.660-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package embassy-domsearch: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing |
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License: DFSG free
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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
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Versions of package emboss |
Release | Version | Architectures |
sid | 6.6.0+dfsg-15 | amd64,arm64,mips64el,ppc64el,riscv64 |
trixie | 6.6.0+dfsg-15 | amd64,arm64,mips64el,ppc64el,riscv64 |
buster | 6.6.0+dfsg-7 | amd64,arm64,armhf,i386 |
bookworm | 6.6.0+dfsg-12 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 6.6.0+dfsg-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 6.6.0+dfsg-1 | amd64,armel,armhf,i386 |
stretch | 6.6.0+dfsg-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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 |
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License: DFSG free
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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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exonerate
generic tool for pairwise sequence comparison
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Versions of package exonerate |
Release | Version | Architectures |
trixie | 2.4.0-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 2.4.0-4 | amd64,arm64,armhf,i386 |
bookworm | 2.4.0-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.4.0-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.4.0-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 2.2.0-6 | amd64,armel,armhf,i386 |
stretch | 2.4.0-2 | amd64,arm64,armel,armhf,i386,mips,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
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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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fastdnaml
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Versions of package fastdnaml |
Release | Version | Architectures |
buster | 1.2.2-14 | amd64,arm64,armhf,i386 |
bullseye | 1.2.2-15 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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 |
jessie | 1.2.2-10 | amd64,armel,armhf,i386 |
stretch | 1.2.2-11 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package fastdnaml: |
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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fastDNAml 源于 3.3 版的 DNAML(作者为 Joseph Felsenstein,是 PHYLIP 软件包的一部分)
程序。在使用此程序时用户可以参阅 DNAML 程序的文档。
fastDNAml 与 DNAML 所解决的问题是一样的,但它运算速度更快、占用内存更少,故可支持更庞大的
进化树或者/以及更多次的 bootstrap 检验。 大部分 fastDNAml 事实上是 PHYLIP 3.3 版 DNAML
程序的改写,由原先的 PASCAL 语言改写为 C 语言。
不过该项目的主页目前已不可访问,可能以后不会有更新。
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fastlink
faster version of pedigree programs of Linkage
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Versions of package fastlink |
Release | Version | Architectures |
bookworm | 4.1P-fix100+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 4.1P-fix100+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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 |
jessie | 4.1P-fix95-3 | amd64,armel,armhf,i386 |
trixie | 4.1P-fix100+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 4.1P-fix100+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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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fastqc
quality control for high throughput sequence data
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Versions of package fastqc |
Release | Version | Architectures |
jessie | 0.11.2+dfsg-3 | all |
sid | 0.12.1+dfsg-4 | all |
trixie | 0.12.1+dfsg-4 | all |
bookworm | 0.11.9+dfsg-6 | all |
bullseye | 0.11.9+dfsg-4 | all |
buster | 0.11.8+dfsg-2 | all |
stretch | 0.11.5+dfsg-6 | all |
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License: DFSG free
|
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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fasttree
phylogenetic trees from alignments of nucleotide or protein sequences
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Versions of package fasttree |
Release | Version | Architectures |
stretch | 2.1.9-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.1.11-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.1.11-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.1.11-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.1.11-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 2.1.7-2 | amd64,armel,armhf,i386 |
buster | 2.1.10-2 | amd64,arm64,armhf,i386 |
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License: DFSG free
|
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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fitgcp
fitting genome coverage distributions with mixture models
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Versions of package fitgcp |
Release | Version | Architectures |
sid | 0.0.20150429-5 | all |
stretch | 0.0.20150429-1 | amd64,arm64,mips64el,ppc64el |
buster | 0.0.20150429-2 | amd64,arm64 |
bookworm | 0.0.20150429-5 | all |
bullseye | 0.0.20150429-4 | all |
trixie | 0.0.20150429-5 | all |
jessie | 0.0.20130418-2 | amd64,i386 |
|
License: DFSG free
|
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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flexbar
flexible barcode and adapter removal for sequencing platforms
|
Versions of package flexbar |
Release | Version | Architectures |
buster | 3.4.0-2 | amd64,arm64,armhf,i386 |
stretch | 2.50-2 | amd64,arm64,armhf,i386,mips,mips64el,mipsel,ppc64el |
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 |
experimental | 3.5.0-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 3.5.0-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 2.50-1 | amd64,armhf,i386 |
bullseye | 3.5.0-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
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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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 |
jessie | 1.0.21-3 | amd64,armel,armhf,i386 |
stretch | 1.0.21-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.21-7 | amd64,arm64,armhf,i386 |
bullseye | 1.0.21-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.0.21-13 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.0.21-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
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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gasic
genome abundance similarity correction
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Versions of package gasic |
Release | Version | Architectures |
bookworm | 0.0.r19-8 | all |
buster | 0.0.r19-4 | amd64 |
bullseye | 0.0.r19-7 | all |
sid | 0.0.r19-8 | all |
trixie | 0.0.r19-8 | all |
jessie | 0.0.r18-2 | amd64 |
stretch | 0.0.r19-1 | amd64 |
|
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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genometools
versatile genome analysis toolkit
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Versions of package genometools |
Release | Version | Architectures |
trixie | 1.6.5+ds-2.2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.5.9+ds-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.5.3-2 | amd64,armel,armhf,i386 |
sid | 1.6.5+ds-2.2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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 |
bookworm-backports | 1.6.5+ds-2~bpo12+1 | 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 |
buster | 1.5.10+ds-3 | amd64,arm64,armhf,i386 |
Debtags of package genometools: |
biology | nuceleic-acids |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
uitoolkit | ncurses |
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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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gff2aplot
pair-wise alignment-plots for genomic sequences in PostScript
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Versions of package gff2aplot |
Release | Version | Architectures |
bullseye | 2.0-13 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.0-11 | amd64,arm64,armhf,i386 |
stretch | 2.0-8 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.0-7 | amd64,armel,armhf,i386 |
bookworm | 2.0-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.0-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,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 |
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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 |
jessie | 0.98d-4 | all |
bullseye | 0.98l-4 | all |
buster | 0.98l-2 | all |
stretch | 0.98d-5 | all |
sid | 0.98l-6 | all |
trixie | 0.98l-6 | 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 |
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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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giira
RNA-Seq driven gene finding incorporating ambiguous reads
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Versions of package giira |
Release | Version | Architectures |
jessie | 0.0.20140210-2 | amd64 |
buster | 0.0.20140625-2 | amd64 |
stretch | 0.0.20140625-1 | amd64 |
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License: DFSG free
|
GIIRA is a gene prediction method that identifies potential coding
regions exclusively based on the mapping of reads from an RNA-Seq
experiment. It was foremost designed for prokaryotic gene prediction
and is able to resolve genes within the expressed region of an operon.
However, it is also applicable to eukaryotes and predicts exon intron
structures as well as alternative isoforms.
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glam2
gapped protein motifs from unaligned sequences
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Versions of package glam2 |
Release | Version | Architectures |
jessie | 1064-3 | amd64,armel,armhf,i386 |
buster | 1064-5 | amd64,arm64,armhf,i386 |
bullseye | 1064-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1064-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1064-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 1064-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 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
|
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 |
buster | 2019-01-24-1 (non-free) | amd64 |
bullseye | 2021-02-22+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
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 |
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 |
Debtags of package gmap: |
field | biology, biology:bioinformatics, biology:structural |
role | program |
use | analysing |
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License: DFSG free
|
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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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 |
jessie | 0.5.3-3 | all |
sid | 0.5.4-6 | all |
trixie | 0.5.4-6 | all |
bookworm | 0.5.4-6 | all |
bullseye | 0.5.4-6 | all |
stretch | 0.5.4-1 | all |
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License: DFSG free
|
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 |
jessie | 5.0.2-1 | amd64,armel,armhf,i386 |
stretch | 2016.1-2 | amd64,arm64,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2019.1-1 | amd64,arm64,armhf,i386 |
bullseye | 2020.6-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2022.5-2 | amd64,arm64,mips64el,ppc64el,s390x |
trixie | 2024.4-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
sid | 2024.4-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
experimental | 2025.0~beta-1 | amd64,arm64,mips64el,ppc64el,riscv64,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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hhsuite
sensitive protein sequence searching based on HMM-HMM alignment
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Versions of package hhsuite |
Release | Version | Architectures |
bookworm | 3.3.0+ds-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
sid | 3.3.0+ds-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
stretch | 3.0~beta2+dfsg-3 | amd64 |
trixie | 3.3.0+ds-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
jessie | 2.0.16-5 | amd64 |
buster | 3.0~beta3+dfsg-3 | amd64 |
bullseye | 3.3.0+ds-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
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License: DFSG free
|
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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hisat2
graph-based alignment of short nucleotide reads to many genomes
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Versions of package hisat2 |
Release | Version | Architectures |
stretch | 2.0.5-1 | amd64 |
bookworm | 2.2.1-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.2.1-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.2.1-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 2.1.0-2 | amd64 |
bullseye | 2.2.1-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
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 |
bookworm | 3.3.2+dfsg-1 | amd64,i386 |
buster | 3.2.1+dfsg-1 | amd64,i386 |
stretch | 3.1b2+dfsg-5 | amd64,i386 |
jessie | 3.1b1-3 | amd64,armel,armhf,i386 |
trixie | 3.4+dfsg-2 | amd64,arm64,i386 |
sid | 3.4+dfsg-2 | amd64,arm64,i386 |
bullseye | 3.3.2+dfsg-1 | amd64,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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idba
iterative De Bruijn Graph short read assemblers
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Versions of package idba |
Release | Version | Architectures |
bookworm | 1.1.3-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.1.2-1 | amd64,armel,armhf,i386 |
stretch | 1.1.3-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.1.3-3 | amd64,arm64,armhf,i386 |
bullseye | 1.1.3-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.1.3-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.1.3-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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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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infernal
inference of RNA secondary structural alignments
|
Versions of package infernal |
Release | Version | Architectures |
stretch | 1.1.2-1 | amd64,i386 |
buster | 1.1.2-2 | amd64,i386 |
bullseye | 1.1.4-1 | amd64,i386 |
bookworm | 1.1.4-1 | amd64,i386 |
trixie | 1.1.5-2 | amd64,arm64,i386 |
sid | 1.1.5-2 | amd64,arm64,i386 |
jessie | 1.1.1-2 | amd64,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.
|
|
jellyfish
count k-mers in DNA sequences
|
Versions of package jellyfish |
Release | Version | Architectures |
stretch | 2.2.6-1 | amd64 |
jessie | 2.1.4-1 | amd64 |
sid | 2.3.1-4 | amd64,arm64,mips64el,riscv64 |
sid | 2.3.1-3 | ppc64el |
trixie | 2.3.1-3 | 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 |
buster | 2.2.10-2 | amd64,arm64 |
|
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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|
kalign
Global and progressive multiple sequence alignment
|
Versions of package kalign |
Release | Version | Architectures |
buster | 2.03+20110620-5 | amd64,arm64,armhf,i386 |
bullseye | 3.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.3.5-1 | 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 |
stretch | 2.03+20110620-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.03+20110620-2 | amd64,armel,armhf,i386 |
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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|
kissplice
Detection of various kinds of polymorphisms in RNA-seq data
|
Versions of package kissplice |
Release | Version | Architectures |
stretch | 2.4.0-p1-1 | amd64,arm64,mips64el,ppc64el |
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 |
sid | 2.6.7-1 | amd64,arm64,mips64el,ppc64el,riscv64 |
buster | 2.4.0-p1-4 | amd64,arm64 |
Debtags of package kissplice: |
biology | nuceleic-acids |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
use | analysing |
works-with | biological-sequence |
|
License: DFSG free
|
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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last-align
genome-scale comparison of biological sequences
|
Versions of package last-align |
Release | Version | Architectures |
jessie | 490-1 | amd64,armel,armhf,i386 |
sid | 1542-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1542-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1447-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1179-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 963-2 | amd64,arm64,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 |
|
License: DFSG free
|
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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loki
MCMC linkage analysis on general pedigrees
|
Versions of package loki |
Release | Version | Architectures |
sid | 2.4.7.4-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.4.7.4-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.4.7.4-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.4.7.4-8 | amd64,arm64,armhf,i386 |
stretch | 2.4.7.4-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.4.7.4-5 | amd64,armel,armhf,i386 |
trixie | 2.4.7.4-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package loki: |
field | biology |
interface | commandline |
role | program |
scope | utility |
use | analysing |
|
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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macs
Model-based Analysis of ChIP-Seq on short reads sequencers
|
Versions of package macs |
Release | Version | Architectures |
sid | 3.0.2-1 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
trixie | 3.0.2-1 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
jessie | 2.0.9.1-1 | amd64,armel,armhf,i386 |
stretch | 2.1.1.20160309-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.1.2.1-1 | amd64,arm64,armhf,i386 |
bullseye | 2.2.7.1-3 | amd64,arm64,armel,armhf,i386,ppc64el,s390x |
bookworm | 2.2.7.1-6 | amd64,arm64,armel,armhf,i386,ppc64el,s390x |
|
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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mafft
Multiple alignment program for amino acid or nucleotide sequences
|
Versions of package mafft |
Release | Version | Architectures |
buster | 7.407-2 | amd64,arm64,armhf,i386 |
trixie | 7.505-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 7.205-1 | amd64,armel,armhf,i386 |
sid | 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 |
bookworm | 7.505-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 7.307-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
upstream | 7.525 |
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 |
|
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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mapsembler2
bioinformatics targeted assembly software
|
Versions of package mapsembler2 |
Release | Version | Architectures |
jessie | 2.1.6+dfsg-1 | amd64,armel,armhf,i386 |
sid | 2.2.4+dfsg1-4 | amd64,arm64,ppc64el,s390x |
trixie | 2.2.4+dfsg1-4 | amd64,arm64,ppc64el,s390x |
bookworm | 2.2.4+dfsg1-4 | amd64,arm64,ppc64el,s390x |
bullseye | 2.2.4+dfsg1-3 | amd64,arm64,ppc64el,s390x |
buster | 2.2.4+dfsg-3 | amd64,arm64,armhf,i386 |
stretch | 2.2.3+dfsg-3 | amd64,arm64,armel,armhf,i386,ppc64el,s390x |
|
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
将短的、定长的多态性DNA序列读段比对到参考序列上
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Versions of package maq |
Release | Version | Architectures |
bullseye | 0.7.1-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.7.1-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.7.1-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.7.1-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 0.7.1-5 | amd64,armel,armhf,i386 |
stretch | 0.7.1-7 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.7.1-8 | amd64,arm64,armhf,i386 |
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(Mapping and Assembly with Quality的简称)是一款用于构建新一代测序仪产生
的短读序列到参考序列的比对组装工具。它特别针对Illumina-Solexa 1G基因分析仪进
行了优化设计,并具备初步处理ABI SOLiD数据的功能。Maq曾被称为mapass2。
Maq的开发在2008年停止,其后继者为BWA和SAMtools。
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melting
compute the melting temperature of nucleic acid duplex
|
Versions of package melting |
Release | Version | Architectures |
buster | 5.2.0-1 | all |
sid | 5.2.0-2 | all |
bullseye | 5.2.0-2 | all |
trixie | 5.2.0-2 | all |
bookworm | 5.2.0-2 | all |
jessie | 4.3.1+dfsg-1 | amd64,armel,armhf,i386 |
stretch | 4.3.1+dfsg-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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 |
|
License: DFSG free
|
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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minia
short-read biological sequence assembler
|
Versions of package minia |
Release | Version | Architectures |
bullseye | 3.2.1+git20200522.4960a99-1 | amd64,arm64,i386,mips64el,ppc64el,s390x |
trixie | 3.2.6-4 | amd64,arm64,mips64el,ppc64el,riscv64 |
jessie | 1.6088-1 | amd64,armel,armhf,i386 |
stretch | 1.6906-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 3.2.6-4 | amd64,arm64,mips64el,ppc64el,riscv64 |
buster | 1.6906-2 | amd64,arm64,armhf,i386 |
bookworm | 3.2.6-3 | amd64,arm64,mips64el,ppc64el |
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License: DFSG free
|
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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mipe
Tools to store PCR-derived data
|
Versions of package mipe |
Release | Version | Architectures |
jessie | 1.1-4 | all |
bullseye | 1.1-9 | all |
trixie | 1.1-9 | all |
sid | 1.1-9 | all |
bookworm | 1.1-9 | all |
stretch | 1.1-5 | all |
buster | 1.1-7 | all |
Debtags of package mipe: |
field | biology, biology:bioinformatics, biology:molecular |
interface | commandline |
role | documentation, program |
scope | utility |
use | organizing |
works-with-format | xml |
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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 |
bullseye | 4.9.6-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 4.9.6-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 4.9.6-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 4.0.2-1 | amd64,armel,armhf,i386 |
buster | 4.9.6-4 | amd64,arm64,armhf,i386 |
trixie | 4.9.6-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 4.9.6-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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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mlv-smile
Find statistically significant patterns in sequences
|
Versions of package mlv-smile |
Release | Version | Architectures |
bookworm | 1.47-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.47-6 | amd64,arm64,armhf,i386 |
sid | 1.47-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.47-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.47-3 | amd64,armel,armhf,i386 |
stretch | 1.47-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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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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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 |
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 |
bookworm | 1.48.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.48.1-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.48.1-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,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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mrbayes
Bayesian Inference of Phylogeny
|
Versions of package mrbayes |
Release | Version | Architectures |
buster | 3.2.6+dfsg-2 | amd64,arm64,armhf,i386 |
stretch | 3.2.6+dfsg-1 | amd64,arm64,armhf,i386 |
bookworm | 3.2.7a-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 3.2.7a-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 3.2.7a-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 3.2.3+dfsg-1 | amd64,armel,armhf,i386 |
bullseye | 3.2.7a-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
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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|
mummer
Efficient sequence alignment of full genomes
|
Versions of package mummer |
Release | Version | Architectures |
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 |
sid | 3.23+dfsg-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 3.23+dfsg-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 3.23+dfsg-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 3.23+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,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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|
muscle
Multiple alignment program of protein sequences
|
Versions of package muscle |
Release | Version | Architectures |
trixie | 5.1.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 5.1.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 3.8.31+dfsg-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 3.8.31-1 | amd64,armel,armhf,i386 |
sid | 5.1.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 3.8.1551-2 | amd64,arm64,armhf,i386 |
bullseye | 3.8.1551-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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 |
buster | 3.2.3-3 | amd64,arm64,armhf,i386 |
sid | 3.2.4-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 3.2.4-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 3.2.4-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 3.2.3-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 3.2.3-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 3.2.2-1 | amd64,armel,armhf,i386 |
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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ncbi-epcr
Tool to test a DNA sequence for the presence of sequence tagged sites
|
Versions of package ncbi-epcr |
Release | Version | Architectures |
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 |
jessie | 2.3.12-1-2 | amd64,armel,armhf,i386 |
stretch | 2.3.12-1-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.3.12-1-7 | amd64,arm64,armhf,i386 |
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-tools-bin
NCBI libraries for biology applications (text-based utilities)
|
Versions of package ncbi-tools-bin |
Release | Version | Architectures |
trixie | 6.1.20170106+dfsg2-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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 |
bookworm | 6.1.20170106+dfsg1-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 6.1.20120620-8 | amd64,armel,armhf,i386 |
stretch | 6.1.20170106+dfsg1-0+deb9u1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 6.1.20170106+dfsg2-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,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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ncoils
coiled coil secondary structure prediction
|
Versions of package ncoils |
Release | Version | Architectures |
stretch | 2002-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,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 |
trixie | 2002-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2002-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
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
|
Versions of package neobio |
Release | Version | Architectures |
jessie | 0.0.20030929-1.1 | all |
buster | 0.0.20030929-4 | all |
sid | 0.0.20030929-6 | all |
trixie | 0.0.20030929-6 | all |
bookworm | 0.0.20030929-6 | all |
bullseye | 0.0.20030929-6 | all |
stretch | 0.0.20030929-2 | all |
|
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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paraclu
Parametric clustering of genomic and transcriptomic features
|
Versions of package paraclu |
Release | Version | Architectures |
jessie | 9-1 | amd64,armel,armhf,i386 |
trixie | 10-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 9-2 | amd64,arm64,armhf,i386 |
bookworm | 10-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 10-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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 |
|
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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parsinsert
Parsimonious Insertion of unclassified sequences into phylogenetic trees
|
Versions of package parsinsert |
Release | Version | Architectures |
bookworm | 1.04-12 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.04-15 | amd64,arm64,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.04-15 | amd64,arm64,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.04-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.04-1 | amd64,armel,armhf,i386 |
bullseye | 1.04-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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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pdb2pqr
Preparation of protein structures for electrostatics calculations
|
Versions of package pdb2pqr |
Release | Version | Architectures |
sid | 3.6.1+dfsg-1 | all |
trixie | 3.6.1+dfsg-1 | all |
bookworm | 3.5.2+dfsg-3 | 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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perm
efficient mapping of short reads with periodic spaced seeds
|
Versions of package perm |
Release | Version | Architectures |
trixie | 0.4.0-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 0.4.0-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.4.0-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.4.0-4 | amd64,arm64,armhf,i386 |
jessie | 0.4.0-1 | amd64,armel,armhf,i386 |
bullseye | 0.4.0-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.4.0-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,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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phyml
Phylogenetic estimation using Maximum Likelihood
|
Versions of package phyml |
Release | Version | Architectures |
jessie | 20120412-2 | amd64,armel,armhf,i386 |
buster | 3.3.20180621-2 | amd64,arm64,armhf,i386 |
bullseye | 3.3.20200621-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.3.20220408-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 3.3.20220408-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 3.3.20220408-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 3.2.0+dfsg-7 | amd64,arm64,armhf,i386 |
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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phyutility
simple analyses or modifications on both phylogenetic trees and data matrices
|
Versions of package phyutility |
Release | Version | Architectures |
bookworm | 2.7.3+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.7.3+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 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 |
buster | 2.7.3+dfsg-2 | amd64,arm64,armhf,i386 |
jessie | 2.7.3-1 | amd64,armel,armhf,i386 |
bullseye | 2.7.3+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
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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picard-tools
Command line tools to manipulate SAM and BAM files
|
Versions of package picard-tools |
Release | Version | Architectures |
jessie | 1.113-1 | all |
trixie | 3.1.1+dfsg-1 | all |
bullseye | 2.24.1+dfsg-1 | all |
bookworm | 2.27.5+dfsg-2 | all |
stretch | 2.8.1+dfsg-1 | all |
buster | 2.18.25+dfsg-2 | amd64 |
sid | 3.1.1+dfsg-1 | all |
upstream | 3.3.0 |
|
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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plink
whole-genome association analysis toolset
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Versions of package plink |
Release | Version | Architectures |
sid | 1.07+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.07-3 | amd64,armel,armhf,i386 |
stretch | 1.07-7 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.07+dfsg-2 | amd64,arm64,armhf,i386 |
bullseye | 1.07+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.07+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,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 |
bullseye | 1.90~b6.21-201019-1 | amd64,armel,armhf,i386,mipsel |
bookworm | 1.90~b6.26-220402-1 | amd64,armel,armhf,i386,mipsel |
trixie | 1.90~b7.2-231211-1 | amd64,armel,armhf,i386 |
sid | 1.90~b7.2-231211-1 | amd64,armel,armhf,i386 |
stretch | 1.90~b3.45-170113-1 | amd64,armel,armhf,i386,mipsel |
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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 |
bullseye | 2.00~a3-210203+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.00~a3.5-220809+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.00~a5.8-231123+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,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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poa
Partial Order Alignment for multiple sequence alignment
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Versions of package poa |
Release | Version | Architectures |
bullseye | 2.0+20060928-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 2.0+20060928-3 | amd64,armel,armhf,i386 |
stretch | 2.0+20060928-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.0+20060928-7 | amd64,arm64,armhf,i386 |
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 |
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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prank
Probabilistic Alignment Kit for DNA, codon and amino-acid sequences
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Versions of package prank |
Release | Version | Architectures |
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 |
sid | 0.0.170427+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 0.0.140110-1 | amd64,armel,armhf,i386 |
buster | 0.0.170427+dfsg-2 | amd64,arm64,armhf,i386 |
stretch | 0.0.150803-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.0.170427+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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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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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 |
buster | 1.0.11-7 | amd64,arm64,armhf,i386 |
bookworm | 1.0.11-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.0.11-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.0.11-2 | amd64,armel,armhf,i386 |
bullseye | 1.0.11-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.0.11-13 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
sid | 1.0.11-13 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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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 |
buster | 2.4.0-2 | amd64,arm64,armhf,i386 |
sid | 2.6.1-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 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 |
jessie | 2.3.6-1 | amd64,armel,armhf,i386 |
stretch | 2.3.7-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.4.0-4 | 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 |
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License: DFSG free
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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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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 |
stretch | 0.4.5-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
buster | 0.5.0+dfsg-3 | amd64,arm64,armhf,i386 |
sid | 0.5.0+dfsg-6 | amd64,i386 |
bullseye | 0.5.0+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.5.0+dfsg-6 | amd64,i386 |
trixie | 0.5.0+dfsg-6 | amd64,i386 |
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License: DFSG free
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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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probcons
PROBabilistic CONSistency-based multiple sequence alignment
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Versions of package probcons |
Release | Version | Architectures |
sid | 1.12-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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 |
Debtags of package probcons: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | comparing |
works-with-format | plaintext |
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License: DFSG free
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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
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Versions of package proda |
Release | Version | Architectures |
buster | 1.0-12 | amd64,arm64,armhf,i386 |
stretch | 1.0-10 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 1.0-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.0-8 | amd64,armel,armhf,i386 |
bullseye | 1.0-13 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.0-13 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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 |
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License: DFSG free
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ProDA 是自动探测和排列具有任意域结构的蛋白质集合的同源区域的系统。给定一个
未排列的序列,ProDA 确认出现在一个或多个序列的所有同源区域,并输出这些区域
的本地多排序集合。
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prodigal
Microbial (bacterial and archaeal) gene finding program
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Versions of package prodigal |
Release | Version | Architectures |
bookworm | 2.6.3-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.6.3-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 2.6.3-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 2.6.3-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.6.3-4 | amd64,arm64,armhf,i386 |
stretch | 2.6.3-1 | amd64,arm64,armel,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.6.1-1 | amd64,armel,i386 |
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License: DFSG free
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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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python3-biomaj3-cli
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Versions of package python3-biomaj3-cli |
Release | Version | Architectures |
trixie | 3.1.11-5 | all |
bookworm | 3.1.11-4 | all |
sid | 3.1.11-5 | all |
buster | 3.1.10-1 | all |
bullseye | 3.1.11-1 | all |
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License: DFSG free
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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 client to execute BioMAJ3 or communicate with the
BioMAJ daemon process (python3-biomaj3-daemon) in case of microservice config.
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python3-biopython
Python3 library for bioinformatics
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Versions of package python3-biopython |
Release | Version | Architectures |
bookworm | 1.80+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.78+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.73+dfsg-1 | amd64,arm64,armhf,i386 |
sid | 1.84+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.84+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.68+dfsg-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.64+dfsg-5 | amd64,armel,armhf,i386 |
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License: DFSG free
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The Biopython Project is an international association
of developers of freely available Python tools for
computational molecular biology.
It is a distributed collaborative effort to develop Python3
libraries and applications which address the needs of
current and future work in bioinformatics. The source code
is made available under the Biopython License, which is
extremely liberal and compatible with almost every license in
the world. The project works along with the Open Bioinformatics
Foundation, who generously provide web and CVS space for
the project.
Please cite:
Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski and Michiel J. L. de Hoon:
Biopython: freely available Python tools for computational molecular biology and bioinformatics.
(PubMed,eprint)
Bioinformatics
25(11):1422-1423
(2009)
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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 | 2024.11.29a2 |
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License: DFSG free
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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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qiime
Quantitative Insights Into Microbial Ecology
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Versions of package qiime |
Release | Version | Architectures |
bullseye | 2020.11.1-1 | all |
bookworm | 2022.11.1-2 | all |
jessie | 1.8.0+dfsg-4 | amd64,armel,armhf,i386 |
sid | 2024.5.0-1 | all |
upstream | 2024.10.1 |
Debtags of package qiime: |
role | program |
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License: DFSG free
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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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|
r-bioc-edger
Empirical analysis of digital gene expression data in R
|
Versions of package r-bioc-edger |
Release | Version | Architectures |
stretch | 3.14.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,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 |
experimental | 4.4.0+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
sid | 4.2.2+dfsg-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
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 |
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.
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|
r-bioc-hilbertvis
GNU R package to visualise long vector data
|
Versions of package r-bioc-hilbertvis |
Release | Version | Architectures |
sid | 1.62.0-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
experimental | 1.64.0-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
jessie | 1.24.0-1 | amd64,armel,armhf,i386 |
trixie | 1.62.0-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.56.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.48.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.40.0-1 | amd64,arm64,armhf,i386 |
stretch | 1.32.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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.
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r-cran-pvclust
Hierarchical Clustering with P-Values via Multiscale Bootstrap
|
Versions of package r-cran-pvclust |
Release | Version | Architectures |
buster | 2.0-0-4 | all |
jessie | 1.3-0-1 | all |
sid | 2.2-0-2 | all |
trixie | 2.2-0-2 | all |
bookworm | 2.2-0-2 | all |
bullseye | 2.2-0-2 | all |
stretch | 2.0-0-1 | all |
|
License: DFSG free
|
pvclust is a package for assessing the uncertainty in
hierarchical cluster analysis. It provides AU (approximately
unbiased) p-values as well as BP (boostrap probability) values
computed via multiscale bootstrap resampling.
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r-cran-qtl
GNU R package for genetic marker linkage analysis
|
Versions of package r-cran-qtl |
Release | Version | Architectures |
buster | 1.44-9-1 | amd64,arm64,armhf,i386 |
sid | 1.70-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.58-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.70-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.33-7-1 | amd64,armel,armhf,i386 |
stretch | 1.40-8-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.47-9-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,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-vegan
Community Ecology Package for R
|
Versions of package r-cran-vegan |
Release | Version | Architectures |
jessie | 2.0-10-1 | amd64,armel,armhf,i386 |
buster | 2.5-4+dfsg-3 | amd64,arm64,armhf,i386 |
bookworm | 2.6-4+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 2.4-2-1 | amd64,arm64,armel,armhf,i386,mips,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 |
bullseye | 2.5-7+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
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-other-mott-happy.hbrem
GNU R package for fine-mapping complex diseases
|
Versions of package r-other-mott-happy.hbrem |
Release | Version | Architectures |
jessie | 2.4-1 | amd64,armel,armhf,i386 |
buster | 2.4-3 | amd64,arm64,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 |
stretch | 2.4-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.4-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.4-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
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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raster3d
tools for generating images of proteins or other molecules
|
Versions of package raster3d |
Release | Version | Architectures |
bookworm | 3.0-7-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 3.0-3-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 3.0-3-5 | amd64,arm64,armhf,i386 |
sid | 3.0-7-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 3.0-3-1 | amd64,armel,armhf,i386 |
bullseye | 3.0-7-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 3.0-7-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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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readseq
Conversion between sequence formats
|
Versions of package readseq |
Release | Version | Architectures |
jessie | 1-11 | amd64,armel,armhf,i386 |
sid | 1-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1-13 | amd64,arm64,armhf,i386 |
stretch | 1-11 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,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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rnahybrid
Fast and effective prediction of microRNA/target duplexes
|
Versions of package rnahybrid |
Release | Version | Architectures |
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 |
bullseye | 2.1.2-6 | 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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rtax
Classification of sequence reads of 16S ribosomal RNA gene
|
Versions of package rtax |
Release | Version | Architectures |
bullseye | 0.984-7 | all |
jessie | 0.984-2 | all |
buster | 0.984-6 | all |
stretch | 0.984-5 | all |
sid | 0.984-8 | all |
trixie | 0.984-8 | all |
bookworm | 0.984-8 | all |
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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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samtools
processing sequence alignments in SAM, BAM and CRAM formats
|
Versions of package samtools |
Release | Version | Architectures |
jessie | 0.1.19-1 | amd64,armhf,i386 |
buster | 1.9-4 | amd64,arm64,armhf |
stretch-backports | 1.7-2~bpo9+1 | amd64,arm64,armel,armhf,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.11-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.16.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.20-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.20-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
experimental | 1.21-0+exp1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.3.1-3 | amd64,arm64,armel,i386,mips64el,mipsel,ppc64el |
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 |
|
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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seqan-apps
C++ library for the analysis of biological sequences
|
Versions of package seqan-apps |
Release | Version | Architectures |
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 |
bullseye | 2.4.0+dfsg-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
experimental | 2.5.0~rc3+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 2.3.1+dfsg-4 | amd64,arm64,i386,mips64el,ppc64el,s390x |
bookworm | 2.4.0+dfsg-15 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.4.0+dfsg-16 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.4.0+dfsg-16 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.4.1+dfsg-2 | amd64,armhf,i386 |
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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sibsim4
align expressed RNA sequences on a DNA template
|
Versions of package sibsim4 |
Release | Version | Architectures |
jessie | 0.20-2 | amd64,armel,armhf,i386 |
stretch | 0.20-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 0.20-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.20-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 0.20-4 | amd64,arm64,armhf,i386 |
bullseye | 0.20-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 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 |
|
License: DFSG free
|
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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sigma-align
Simple greedy multiple alignment of non-coding DNA sequences
|
Versions of package sigma-align |
Release | Version | Architectures |
bullseye | 1.1.3-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.1.3-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.1.3-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.1.3-3 | amd64,armel,armhf,i386 |
stretch | 1.1.3-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.1.3-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.1.3-6 | amd64,arm64,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
|
Versions of package sim4 |
Release | Version | Architectures |
buster | 0.0.20121010-5 | amd64,arm64,armhf,i386 |
trixie | 0.0.20121010-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 0.0.20121010-1 | amd64,armel,armhf,i386 |
sid | 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 |
bullseye | 0.0.20121010-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 0.0.20121010-4 | amd64,arm64,armel,armhf,i386,mips,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.
|
|
smalt
Sequence Mapping and Alignment Tool
|
Versions of package smalt |
Release | Version | Architectures |
bookworm | 0.7.6-12 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.7.6-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.7.6-8 | amd64,arm64,armhf |
stretch | 0.7.6-6 | amd64,arm64,armel,i386,mips64el,mipsel,ppc64el |
jessie | 0.7.6-4 | amd64,armhf,i386 |
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 |
|
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.
|
|
snap
location of genes from DNA sequence with hidden markov model
|
Versions of package snap |
Release | Version | Architectures |
trixie | 2013-11-29-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 2013-11-29-1 | amd64,armel,armhf,i386 |
stretch | 2013-11-29-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 2013-11-29-11 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 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 |
buster | 2013-11-29-9 | amd64,arm64,armhf,i386 |
|
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.
|
|
soapdenovo
short-read assembly method to build de novo draft assembly
|
Versions of package soapdenovo |
Release | Version | Architectures |
stretch | 1.05-3 | amd64 |
sid | 1.05-6 | amd64 |
trixie | 1.05-6 | amd64 |
bookworm | 1.05-6 | amd64 |
bullseye | 1.05-6 | amd64 |
buster | 1.05-5 | amd64 |
jessie | 1.05-2 | 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.
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)
|
|
soapdenovo2
short-read assembly method to build de novo draft assembly
|
Versions of package soapdenovo2 |
Release | Version | Architectures |
buster | 241+dfsg-3 | amd64 |
trixie | 242+dfsg-4 | amd64 |
sid | 242+dfsg-4 | amd64 |
bookworm | 242+dfsg-3 | amd64 |
bullseye | 242+dfsg-1 | amd64 |
stretch | 240+dfsg1-2 | amd64 |
jessie | 240+dfsg-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)
|
|
sra-toolkit
utilities for the NCBI Sequence Read Archive
|
Versions of package sra-toolkit |
Release | Version | Architectures |
bookworm | 3.0.3+dfsg-6~deb12u1 | amd64,arm64 |
sid | 3.0.9+dfsg-7 | amd64,arm64 |
trixie | 3.0.9+dfsg-7 | amd64,arm64 |
buster | 2.9.3+dfsg-1 | amd64 |
bullseye | 2.10.9+dfsg-2 | amd64 |
stretch | 2.8.1-2+dfsg-2 | amd64,i386 |
jessie | 2.3.5-2+dfsg-1 | amd64,i386 |
upstream | 3.1.1 |
|
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)
|
|
ssake
genomics application for assembling millions of very short DNA sequences
|
Versions of package ssake |
Release | Version | Architectures |
jessie | 3.8.2-1 | all |
sid | 4.0.1-2 | all |
trixie | 4.0.1-2 | all |
bookworm | 4.0.1-1 | all |
bullseye | 4.0-3 | all |
buster | 4.0-2 | all |
stretch | 3.8.4-1 | all |
Debtags of package ssake: |
biology | nuceleic-acids |
field | biology |
interface | shell |
role | program |
scope | utility |
use | analysing |
|
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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|
staden-io-lib-utils
programs for manipulating DNA sequencing files
|
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 |
bullseye | 1.14.13-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.14.15-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.13.7-1 | amd64,armel,armhf,i386 |
Debtags of package staden-io-lib-utils: |
biology | nuceleic-acids, peptidic |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing |
|
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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|
t-coffee
Multiple Sequence Alignment
|
Versions of package t-coffee |
Release | Version | Architectures |
sid | 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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 |
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.
|
|
tabix
generic indexer for TAB-delimited genome position files
|
Versions of package tabix |
Release | Version | Architectures |
buster | 1.9-12~deb10u1 | amd64,arm64,armhf,i386 |
stretch | 1.3.2-2 | amd64,arm64,armel,i386,mips64el,mipsel,ppc64el |
stretch-backports | 1.7-2~bpo9+1 | amd64,arm64,armel,armhf,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.1-1 | amd64,armel,i386 |
bullseye | 1.11-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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 |
jessie | 0.2.6-2 | armhf |
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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|
theseus
superimpose macromolecules using maximum likelihood
|
Versions of package theseus |
Release | Version | Architectures |
stretch | 3.3.0-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 3.0.0-1 | amd64,armel,armhf,i386 |
buster | 3.3.0-8 | amd64,arm64,armhf,i386 |
bullseye | 3.3.0-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.3.0-14 | amd64,i386 |
trixie | 3.3.0-14 | amd64,i386 |
sid | 3.3.0-14 | amd64,i386 |
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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|
tigr-glimmer
Gene detection in archea and bacteria
|
Versions of package tigr-glimmer |
Release | Version | Architectures |
jessie | 3.02-3 | amd64,armel,armhf,i386 |
stretch | 3.02b-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 3.02b-2 | amd64,arm64,armhf,i386 |
bullseye | 3.02b-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.02b-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 3.02b-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 3.02b-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,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.
|
|
tree-ppuzzle
Parallelized reconstruction of phylogenetic trees by maximum likelihood
|
Versions of package tree-ppuzzle |
Release | Version | Architectures |
bullseye | 5.3~rc16+dfsg-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 5.3~rc16+dfsg-12 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 5.2-11 | amd64,arm64,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 |
jessie | 5.2-7 | amd64,armel,armhf,i386 |
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 |
|
License: DFSG free
|
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.
|
|
tree-puzzle
Reconstruction of phylogenetic trees by maximum likelihood
|
Versions of package tree-puzzle |
Release | Version | Architectures |
sid | 5.3~rc16+dfsg-12 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 5.3~rc16+dfsg-12 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 5.3~rc16+dfsg-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 5.3~rc16+dfsg-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 5.2-11 | amd64,arm64,armhf,i386 |
stretch | 5.2-8 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 5.2-7 | amd64,armel,armhf,i386 |
Debtags of package tree-puzzle: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing, comparing |
works-with-format | plaintext |
|
License: DFSG free
|
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.
|
|
vcftools
Collection of tools to work with VCF files
|
Versions of package vcftools |
Release | Version | Architectures |
jessie | 0.1.12+dfsg-1 | amd64,armel,armhf,i386 |
sid | 0.1.16-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 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 |
bullseye | 0.1.16-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.1.16-1 | amd64,arm64,armhf,i386 |
stretch | 0.1.14+dfsg-4+deb9u1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie-security | 0.1.12+dfsg-1+deb8u1 | amd64,armel,armhf,i386 |
Debtags of package vcftools: |
role | program |
|
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)
|
|
velvet
Nucleic acid sequence assembler for very short reads
|
Versions of package velvet |
Release | Version | Architectures |
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 |
sid | 1.2.10+dfsg1-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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 |
bullseye | 1.2.10+dfsg1-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.2.10+dfsg1-1 | amd64,armel,armhf,i386 |
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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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
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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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wise
comparison of biopolymers, like DNA and protein sequences
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Versions of package wise |
Release | Version | Architectures |
bookworm | 2.4.1-23 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.4.1-23 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 2.4.1-17 | amd64,armel,armhf,i386 |
stretch | 2.4.1-19 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2.4.1-25 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 2.4.1-21 | amd64,arm64,armhf,i386 |
trixie | 2.4.1-25 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package wise: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | comparing |
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License: DFSG free
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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.
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Debian packages in contrib or non-free
cufflinks
Transcript assembly, differential expression and regulation for RNA-Seq
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Versions of package cufflinks |
Release | Version | Architectures |
trixie | 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 |
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 |
stretch | 2.2.1-3 (non-free) | amd64 |
jessie | 2.2.1-1 (non-free) | amd64 |
sid | 2.2.1+dfsg.1-10 (non-free) | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: non-free
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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.
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embassy-phylip
EMBOSS conversions of the programs in the phylip package
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Versions of package embassy-phylip |
Release | Version | Architectures |
buster | 3.69.660-3 (non-free) | amd64 |
jessie | 3.69.650-2 (non-free) | amd64 |
stretch | 3.69.660-1 (non-free) | amd64 |
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License: non-free
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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.
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Packaging has started and developers might try the packaging code in VCS
bagpipe
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Versions of package bagpipe |
Release | Version | Architectures |
VCS | 2012.02.15-1 | all |
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License: GPL3+
Debian package not available
Version: 2012.02.15-1
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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.
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