Debian Med Biology packages

License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: abacas-examples

Please cite: Samuel Assefa, Thomas M. Keane, Thomas D. Otto, Chris Newbold and Matthew Berriman: ABACAS: algorithm-based automatic contiguation of assembled sequences. (PubMed,eprint) Bioinformatics 25(15):1968-1969 (2009)

Topics: Probes and primers

abpoa

??? missing short description for package abpoa :-(

https://github.com/yangao07/abPOA

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package abpoa
Release	Version	Architectures
bookworm	1.4.1-3	amd64,arm64,ppc64el
forky	1.5.6-1	amd64,arm64,ppc64el
trixie	1.5.3-1	amd64,arm64,ppc64el
sid	1.5.6-1	amd64,arm64,loong64,ppc64el

Popcon: 6 users (39 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Yan Gao, Yongzhuang Liu, Yanmei Ma, Bo Liu, Yadong Wang and Yi Xing: abPOA: an SIMD-based C library for fast partial order alignment using adaptive band. Bioinformatics 37(15):2209–2211 (2021)

abyss

??? missing short description for package abyss :-(

https://github.com/bcgsc/abyss

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package abyss
Release	Version	Architectures
sid	2.3.10-2	amd64,arm64,loong64,ppc64el,riscv64,s390x
trixie	2.3.10-1	amd64,arm64,ppc64el,riscv64,s390x
forky	2.3.10-2	amd64,arm64,ppc64el,riscv64,s390x
bullseye	2.2.5+dfsg-1	amd64,arm64,armhf,i386
bookworm	2.3.5+dfsg-2	amd64,arm64,mips64el,ppc64el,s390x

Popcon: 7 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

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)

Registry entries: Bio.tools SciCrunch Bioconda

Topics: Sequence assembly

acedb-other

??? missing short description for package acedb-other :-(

http://www.acedb.org/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package acedb-other
Release	Version	Architectures
sid	4.9.39+dfsg.02-9	amd64,arm64,armhf,i386,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,armhf,i386

Popcon: 1 users (0 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: L. D. Stein and J. Thierry-Mieg: AceDB: a genome database management system. Computing in Science and Engineering 1(3):44-52 (1999)

Registry entries: Bio.tools

adapterremoval

??? missing short description for package adapterremoval :-(

https://github.com/MikkelSchubert/adapterremoval

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package adapterremoval
Release	Version	Architectures
forky	2.3.4-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2.3.1-3	amd64,arm64,armhf,i386
sid	2.3.4-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	2.3.3-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	2.3.4-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
upstream	3.0.0

Popcon: 5 users (35 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: multiqc

Please cite: Mikkel Schubert, Stinus Lindgreen and Ludovic Orlando: AdapterRemoval v2: rapid adapter trimming, identification, and read merging. (PubMed,eprint) BMC Research Notes 9:88 (2016)

Registry entries: SciCrunch

adun-core

??? missing short description for package adun-core :-(

http://wiki.gnustep.org/index.php/Adun

Maintainer: Debian Med Packaging Team (Yavor Doganov)

Versions of package adun-core
Release	Version	Architectures
sid	0.81-15	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	0.81-15	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
trixie	0.81-15	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	0.81-14	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	0.81-14	amd64,arm64,armhf,i386

Popcon: 10 users (35 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Michael A. Johnston, Ignacio Fdez. Galván and Jordi Villà-Freixa: Framework-based design of a new all-purpose molecular simulation application: The Adun simulator. (PubMed) J. Comp. Chem. 26(15):1647-1659 (2005)

aegean

??? missing short description for package aegean :-(

https://standage.github.io/AEGeAn

Maintainer: Debian Med Packaging Team (Sascha Steinbiss)

Versions of package aegean
Release	Version	Architectures
sid	0.16.0+dfsg-5	amd64,arm64,armhf,i386,loong64,ppc64el,s390x
forky	0.16.0+dfsg-5	amd64,arm64,armhf,i386,loong64,ppc64el,s390x
trixie	0.16.0+dfsg-4	amd64,arm64,armel,armhf,i386,ppc64el,s390x
bookworm	0.16.0+dfsg-2	amd64,arm64,armel,armhf,i386,mipsel,ppc64el,s390x
bullseye	0.16.0+dfsg-2	amd64,arm64,armhf,i386

Popcon: 4 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Daniel S Standage and Volker P Brendel: ParsEval: parallel comparison and analysis of gene structure annotations.. (PubMed,eprint) BMC Bioinformatics 13(1):187 (2012)

Topics: Sequencing

aevol

??? missing short description for package aevol :-(

https://www.aevol.fr/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package aevol
Release	Version	Architectures
bullseye	5.0+ds-2	amd64,arm64,armhf,i386
bookworm	5.0+ds-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	5.0+ds-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	9.3.0-1	amd64,arm64,loong64,ppc64el,riscv64,s390x
upstream	9.4.0

Popcon: 9 users (32 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

alien-hunter

??? missing short description for package alien-hunter :-(

https://www.sanger.ac.uk/science/tools/alien-hunter

Maintainer: Debian Med Packaging Team (Pierre Gruet)

Popcon: 7 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Georgios S. Vernikos and Julian Parkhill: Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. (PubMed,eprint) Bioinformatics 22(18):2196-2203 (2006)

Registry entries: SciCrunch

alter-sequence-alignment

??? missing short description for package alter-sequence-alignment :-(

http://sing.ei.uvigo.es/ALTER/

Maintainer: Debian Med Packaging Team (Charles Plessy)

Versions of package alter-sequence-alignment
Release	Version	Architectures
forky	1.3.4-8	all
bookworm	1.3.4-6	all
sid	1.3.4-8	all
bullseye	1.3.4-4	all
trixie	1.3.4-8	all

Popcon: 6 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Daniel Glez-Peña, Daniel Gómez-Blanco, Miguel Reboiro-Jato, Florentino Fdez-Riverola and David Posada: ALTER: program-oriented conversion of DNA and protein alignments". (PubMed,eprint) Nucl. Acids Res. 38(suppl 2):W14-W18 (2010)

Registry entries: Bio.tools SciCrunch

altree

??? missing short description for package altree :-(

https://gitlab.inria.fr/NGS/ALTree

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package altree
Release	Version	Architectures
sid	1.3.2-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.3.2-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.3.2-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.3.2-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.3.1-10	amd64,arm64,armhf,i386

Debtags of package altree:
field	biology, biology:bioinformatics
interface	commandline
role	program, shared-lib
scope	utility
use	analysing, comparing
works-with-format	plaintext

Popcon: 7 users (32 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Claire Bardel, Vincent Danjean and Emmanuelle Genin: ALTree: association detection and localization of susceptibility sites using haplotype phylogenetic trees. (PubMed,eprint) Bioinformatics 22(11):1402-1403 (2006)

Registry entries: SciCrunch

amap-align

??? missing short description for package amap-align :-(

https://github.com/mes5k/amap-align

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package amap-align
Release	Version	Architectures
trixie	2.2+git20080214.600fc29+dfsg-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	2.2+git20080214.600fc29+dfsg-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	2.2+git20080214.600fc29+dfsg-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	2.2+git20080214.600fc29+dfsg-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	2.2+git20080214.600fc29+dfsg-2	amd64,arm64,armhf,i386

Debtags of package amap-align:
field	biology, biology:bioinformatics
interface	commandline
role	program
scope	utility
use	analysing, comparing
works-with-format	plaintext

Popcon: 13 users (37 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Ariel S. Schwartz and Lior Pachter: Multiple alignment by sequence annealing. (eprint) Bioinformatics 23(2):e24-e29 (2007)

Registry entries: SciCrunch Bioconda

Remark of Debian Med team: Dead upstream

The homepage of this project vanished as well as the Download area. An old unmaintained version remained at code.google.com. Please drop the maintainer a note if you have any news of this project.

ampliconnoise

??? missing short description for package ampliconnoise :-(

https://github.com/lanzen/ampliconnoise

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package ampliconnoise
Release	Version	Architectures
bullseye	1.29-9	amd64,arm64,armhf,i386
bookworm	1.29-10	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.29-17	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.29-17	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
trixie	1.29-15	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 10 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Christopher Quince, Anders Lanzen, Russell J Davenport and Peter J Turnbaugh: Removing Noise From Pyrosequenced Amplicons. (PubMed,eprint) BMC Bioinformatics 12:38 (2011)

Registry entries: Bio.tools SciCrunch

Topics: Sequencing

andi

??? missing short description for package andi :-(

https://github.com/EvolBioInf/andi

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package andi
Release	Version	Architectures
trixie	0.14-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	0.13-3	amd64,arm64,armhf,i386
bookworm	0.14-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	0.14-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	0.14-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
upstream	1.15

Popcon: 5 users (34 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: Bernhard Haubold, Fabian Klötzl and Peter Pfaffelhuber: andi: Fast and accurate estimation of evolutionary distances between closely related genomes. (PubMed,eprint) Bioinformatics 31(8):1169-1175 (2015)

Registry entries: Bio.tools Bioconda

Topics: Phylogenetics

anfo

??? missing short description for package anfo :-(

https://bioinf.eva.mpg.de/anfo/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Popcon: 1 users (0 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Registry entries: SciCrunch

Topics: Sequencing

any2fasta

??? missing short description for package any2fasta :-(

https://github.com/tseemann/any2fasta

Maintainer: Debian Med Packaging Team (Andreas Tille)

Popcon: 5 users (36 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

aragorn

??? missing short description for package aragorn :-(

http://mbio-serv2.mbioekol.lu.se/ARAGORN/

Maintainer: Debian Med Packaging Team (Sascha Steinbiss)

Versions of package aragorn
Release	Version	Architectures
bookworm	1.2.38-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.2.41-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.2.41-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.2.41-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	1.2.38-4	amd64,arm64,armhf,i386

Popcon: 7 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Dean Laslett and Bjorn Canback: ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. (PubMed,eprint) Nucleic Acids Research 32(1):11-16 (2004)

Registry entries: SciCrunch Bioconda

Topics: Functional, regulatory and non-coding RNA

arden

??? missing short description for package arden :-(

http://sourceforge.net/projects/arden/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Popcon: 7 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Sven H. Giese, Franziska Zickmann and Bernhard Y. Renard: Specificity control for read alignments using an artificial reference genome-guided false discovery rate. (PubMed,eprint) Bioinformatics 30(1):9-16 (2013)

Registry entries: SciCrunch

Topics: Sequencing

ariba

??? missing short description for package ariba :-(

https://github.com/sanger-pathogens/ariba

Maintainer: Debian Med Packaging Team (Alexandre Detiste)

Versions of package ariba
Release	Version	Architectures
bullseye	2.14.6+ds-1	amd64,arm64
sid	2.14.7+ds-12	amd64,arm64,loong64,ppc64el,riscv64
trixie	2.14.7+ds-7	amd64,arm64,ppc64el,riscv64
forky	2.14.7+ds-12	amd64,arm64,loong64,ppc64el,riscv64
bookworm	2.14.6+ds-5	amd64,arm64,mips64el,ppc64el

Popcon: 5 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Martin Hunt, Alison E. Mather, Leonor Sanchez-Buso, Andrew J. Page, Julian Parkhill, Jacqueline A. Keane and Simon R. Harris: ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads. (PubMed,eprint) Microbial Genomics 3 (2017)

Registry entries: SciCrunch Bioconda

art-nextgen-simulation-tools

??? missing short description for package art-nextgen-simulation-tools :-(

https://www.niehs.nih.gov/research/resources/software/biostatistics/art/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package art-nextgen-simulation-tools
Release	Version	Architectures
trixie	20160605+dfsg-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	20160605+dfsg-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	20160605+dfsg-4	amd64,arm64,armhf,i386
sid	20160605+dfsg-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	20160605+dfsg-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 6 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Weichun Huang, Leping Li, Jason R. Myers and Gabor T. Marth: ART: a next-generation sequencing read simulator. (PubMed,eprint) Bioinformatics 28(4):593-594 (2012)

Registry entries: SciCrunch Bioconda

artemis

??? missing short description for package artemis :-(

https://sanger-pathogens.github.io/Artemis/Artemis/

Maintainer: Debian Med Packaging Team (Pierre Gruet)

Versions of package artemis
Release	Version	Architectures
bullseye	18.1.0+dfsg-3	amd64
bookworm	18.2.0+dfsg-3	all
trixie	18.2.0+dfsg-4	all
forky	18.2.0+dfsg-5	all
sid	18.2.0+dfsg-5	all

Popcon: 12 users (31 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Tim Carver, Simon R. Harris, Matthew Berriman, Julian Parkhill and Jacqueline A. McQuillan: Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. (PubMed,eprint) Bioinformatics 28(4):464-469 (2012)

Registry entries: Bio.tools SciCrunch Bioconda

Topics: Genomics

artfastqgenerator

??? missing short description for package artfastqgenerator :-(

https://sourceforge.net/projects/artfastqgen/

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package artfastqgenerator
Release	Version	Architectures
trixie	0.0.20150519-5	all
forky	0.0.20150519-6	all
sid	0.0.20150519-6	all
bullseye	0.0.20150519-4	all
bookworm	0.0.20150519-4	all

Popcon: 4 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Matthew Frampton and Richard Houlston: Generation of Artificial FASTQ Files to Evaluate the Performance of Next-Generation Sequencing Pipelines. (PubMed,eprint) PLOSone 7(11):e49110 (2012)

assembly-stats

??? missing short description for package assembly-stats :-(

https://github.com/sanger-pathogens/assembly-stats

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package assembly-stats
Release	Version	Architectures
forky	1.0.1+ds-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.0.1+ds-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	1.0.1+ds-3	amd64,arm64,armhf,i386
bookworm	1.0.1+ds-6	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.0.1+ds-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 5 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

assemblytics

??? missing short description for package assemblytics :-(

http://assemblytics.com/

Maintainer: Debian Med Packaging Team (ikeadeoyin)

Versions of package assemblytics
Release	Version	Architectures
bullseye	1.0+ds-2	all
bookworm	1.2.1+dfsg-1	all
trixie	1.2.1+dfsg-2	all
sid	1.2.1+dfsg-2	all
upstream	1.2.2

Popcon: 5 users (34 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: Maria Nattestad and Michael C. Schatz: Assemblytics: a web analytics tool for the detection of variants from an assembly. (PubMed) Bioinformatics 32(19):3021-3023 (2016)

atac

??? missing short description for package atac :-(

http://kmer.sourceforge.net

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package atac
Release	Version	Architectures
sid	0~20150903+r2013-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	0~20150903+r2013-8	amd64,arm64,armhf,i386
bookworm	0~20150903+r2013-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	0~20150903+r2013-9	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	0~20150903+r2013-10	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x

Popcon: 6 users (38 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: kmer-examples

Please cite: B. Walenz and L. Florea: Sim4db and leaff: Utilities for fast batched spliced alignment and sequence indexing. (PubMed) Bioinformatics 27(13):1869-1870 (2011)

Registry entries: Bio.tools SciCrunch Bioconda

ataqv

??? missing short description for package ataqv :-(

https://github.com/ParkerLab/ataqv/

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package ataqv
Release	Version	Architectures
forky	1.3.1+ds-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
trixie	1.3.1+ds-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64
bullseye	1.2.1+ds-1	amd64,arm64,armhf,i386
sid	1.3.1+ds-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
bookworm	1.3.0+ds-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el

Popcon: 7 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Peter Orchard, Yasuhiro Kyono, John Hensley, Jacob O. Kitzman and Stephen C.J. Parker: Quantification, Dynamic Visualization, and Validation of Bias in ATAC-Seq Data with ataqv. (eprint) Cell Systems 10(3):2405-4712 (2020)

atropos

??? missing short description for package atropos :-(

https://github.com/jdidion/atropos

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package atropos
Release	Version	Architectures
bullseye	1.1.29+dfsg-1	amd64,arm64,armhf,i386
forky	1.1.32+dfsg-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
bookworm	1.1.31+dfsg-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el
sid	1.1.32+dfsg-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
trixie	1.1.32+dfsg-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64

Popcon: 8 users (35 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: John P. Didion, Marcel Martin and Francis S. Collins: Atropos: specific, sensitive, and speedy trimming of sequencing reads. (PubMed,eprint) PeerJ 5:e3720 (2017)

Registry entries: Bio.tools Bioconda

augur

??? missing short description for package augur :-(

https://github.com/nextstrain/augur

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package augur
Release	Version	Architectures
trixie	24.4.0-1	all
bullseye	11.0.0-1	all
sid	24.4.0-3	all
forky	24.4.0-3	all
bookworm	20.0.0-1	all
upstream	33.2.0

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Git

augustus

??? missing short description for package augustus :-(

https://bioinf.uni-greifswald.de/augustus/

Maintainer: Debian Med Packaging Team (Sascha Steinbiss)

Versions of package augustus
Release	Version	Architectures
bookworm	3.5.0+dfsg-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	3.5.0+dfsg-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	3.5.0+dfsg-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	3.4.0+dfsg2-2	amd64,arm64,armhf,i386
sid	3.5.0+dfsg-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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autodock

??? missing short description for package autodock :-(

http://autodock.scripps.edu/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package autodock
Release	Version	Architectures
sid	4.2.6-9	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	4.2.6-8	amd64,arm64,armhf,i386
bookworm	4.2.6-9	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	4.2.6-9	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	4.2.6-9	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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The package is enhanced by the following packages: autogrid

autodock-vina

??? missing short description for package autodock-vina :-(

https://vina.scripps.edu

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package autodock-vina
Release	Version	Architectures
sid	1.2.7-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.2.7-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.2.7-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.2.3-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.1.2-6	amd64,arm64,armhf,i386

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Please cite: Oleg Trott and Arthur J. Olson: AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. (eprint) Journal of Computational Chemistry 31(2):455-461 (2010)

Registry entries: Bio.tools SciCrunch Bioconda

autogrid

??? missing short description for package autogrid :-(

http://autodock.scripps.edu/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package autogrid
Release	Version	Architectures
bookworm	4.2.6-9	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	4.2.6-9	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	4.2.6-9	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	4.2.6-8	amd64,arm64,armhf,i386
sid	4.2.6-9	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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avogadro

??? missing short description for package avogadro :-(

https://avogadro.cc/

Maintainer: Debichem Team (Drew Parsons)

Versions of package avogadro
Release	Version	Architectures
sid	1.101.0-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.101.0-1	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.97.0-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.100.0-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	1.93.0-2	amd64,arm64,armhf,i386
upstream	2.0.0

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Please cite: Marcus D Hanwell, Donald E Curtis, David C Lonie, Tim Vandermeersch, Eva Zurek and Geoffrey R Hutchison: Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. (eprint) J. Cheminf. 4:17 (2012)

Registry entries: Bio.tools SciCrunch

axe-demultiplexer

??? missing short description for package axe-demultiplexer :-(

https://github.com/kdmurray91/axe

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package axe-demultiplexer
Release	Version	Architectures
sid	0.3.3+dfsg-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	0.3.3+dfsg-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	0.3.3+dfsg-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	0.3.3+dfsg-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	0.3.3+dfsg-3	amd64,arm64,armhf,i386

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License: DFSG free

Official Debian package

Git

Registry entries: SciCrunch

baitfisher

??? missing short description for package baitfisher :-(

https://github.com/cmayer/BaitFisher-package

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package baitfisher
Release	Version	Architectures
sid	1.2.7+git20211020.de26d5c+dfsg-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.2.7+git20190123.241d060+dfsg-1	amd64,arm64,armhf,i386
bookworm	1.2.7+git20211020.de26d5c+dfsg-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.2.7+git20211020.de26d5c+dfsg-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.2.7+git20211020.de26d5c+dfsg-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

Please cite: Christoph Mayer, Manuela Sann, Alexander Donath, Martin Meixner, Lars Podsiadlowski, Ralph S. Peters, Malte Petersen, Karen Meusemann, Karsten Liere, Johann-Wolfgang Wägele, Bernhard Misof, Christoph Bleidorn, Michael Ohl and Oliver Niehuis: BaitFisher: A Software Package for Multispecies Target DNA Enrichment Probe Design. (PubMed,eprint) Mol. Biol. Evol. 33(7):1875-1886 (2016)

Registry entries: SciCrunch Bioconda

bali-phy

??? missing short description for package bali-phy :-(

http://www.bali-phy.org

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package bali-phy
Release	Version	Architectures
forky	4.1+dfsg-1	amd64,arm64,i386,loong64,ppc64el,riscv64,s390x
trixie	4.0-1	amd64,arm64,i386,ppc64el,riscv64,s390x
bullseye	3.6.0+dfsg-1	amd64,arm64,armhf,i386
experimental	4.0~beta2+dfsg-1	armhf
bookworm	3.6.1+dfsg-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	4.1+dfsg-1	amd64,arm64,i386,loong64,ppc64el,riscv64,s390x
experimental	4.0~beta16+dfsg-1	amd64,arm64,i386,ppc64el,riscv64,s390x
upstream	4.2

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Please cite: Benjamin D. Redelings and Marc A. Suchard: Joint Bayesian Estimation of Alignment and Phylogeny. (PubMed,eprint) Systematic Biology 54(3):401-418 (2005)

Registry entries: Bio.tools

ballview

??? missing short description for package ballview :-(

http://www.ball-project.org/

Maintainer: Debian Med Packaging Team (Yavor Doganov)

Versions of package ballview
Release	Version	Architectures
bookworm	1.5.0+git20180813.37fc53c-11	amd64,arm64,i386,mips64el,mipsel,ppc64el,s390x
sid	1.5.0+git20220524.d85d2dd-2	amd64,arm64,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.5.0+git20180813.37fc53c-6	amd64,arm64,i386

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License: DFSG free

Official Debian package

Git

Please cite: Andreas Moll, Andreas Hildebrandt, Hans-Peter Lenhof and Oliver Kohlbacher: BALLView: a tool for research and education in molecular modeling. (PubMed,eprint) Bioinformatics 22(3):365-366 (2006)

Registry entries: SciCrunch

bamclipper

??? missing short description for package bamclipper :-(

https://github.com/tommyau/bamclipper

Maintainer: Debian Med Packaging Team (Andreas Tille)

Popcon: 2 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Chun Hang Au, Dona N Ho, Ava Kwong, Tsun Leung Chan and Edmond S K Ma: BAMClipper: removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing. (PubMed,eprint) Scientific Reports 7(1):1567 (2017)

Registry entries: Bioconda

bamkit

??? missing short description for package bamkit :-(

https://github.com/hall-lab/bamkit

Maintainer: Debian Med Packaging Team (Shruti Sridhar)

Versions of package bamkit
Release	Version	Architectures
bookworm	0.0.1+git20170413.ccd079d-3	all
trixie	0.0.1+git20170413.ccd079d-3	all
sid	0.0.1+git20170413.ccd079d-3	all
forky	0.0.1+git20170413.ccd079d-3	all
bullseye	0.0.1+git20170413.ccd079d-2	all

Popcon: 9 users (33 upd.)^*

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License: DFSG free

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Git

bamtools

??? missing short description for package bamtools :-(

https://github.com/pezmaster31/bamtools/wiki

Maintainer: Debian Med Packaging Team (Timo Röhling)

Versions of package bamtools
Release	Version	Architectures
bullseye	2.5.1+dfsg-9	amd64,arm64,armhf,i386
bookworm	2.5.2+dfsg-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	2.5.3+dfsg-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	2.5.2+dfsg-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	2.5.3+dfsg-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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The package is enhanced by the following packages: multiqc

Please cite: Derek W. Barnett, Erik K. Garrison, Aaron R. Quinlan, Michael P. Stromberg and Gabor T. Marth: BamTools: a C++ API and toolkit for analyzing and managing BAM files. (PubMed,eprint) Bioinformatics 27(12):1691-2 (2011)

Registry entries: Bio.tools SciCrunch Bioconda

bandage

??? missing short description for package bandage :-(

https://rrwick.github.io/Bandage

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package bandage
Release	Version	Architectures
sid	0.9.0-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	0.9.0-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	0.8.1-4	amd64,arm64,armhf,i386
bookworm	0.9.0-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	0.9.0-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 5 users (34 upd.)^*

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License: DFSG free

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Git

The package is enhanced by the following packages: bandage-examples

Please cite: Ryan R. Wick, Mark B. Schultz, Justin Zobel and Kathryn E. Holt: Bandage: interactive visualisation of de novo genome assemblies. (PubMed,eprint) Bioinformatics 31(20):3350-3352 (2015)

Registry entries: Bio.tools Bioconda

barrnap

??? missing short description for package barrnap :-(

http://www.vicbioinformatics.com/software.barrnap.shtml

Maintainer: Debian Med Packaging Team (Sascha Steinbiss)

Versions of package barrnap
Release	Version	Architectures
bookworm	0.9+dfsg-3	all
forky	1.0.0-2	all
sid	1.0.0-2	all
bullseye	0.9+dfsg-2	all
trixie	0.9+dfsg-4	all
upstream	1.10.6

Popcon: 4 users (35 upd.)^*

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Official Debian package

Git

Registry entries: Bio.tools SciCrunch Bioconda

Topics: Functional, regulatory and non-coding RNA

bbmap

??? missing short description for package bbmap :-(

https://sourceforge.net/projects/bbmap/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package bbmap
Release	Version	Architectures
forky	39.20+dfsg-3	all
bookworm	39.01+dfsg-2	all
bullseye	38.90+dfsg-1	all
sid	39.20+dfsg-3	all
trixie	39.20+dfsg-2	all
upstream	39.84

Popcon: 8 users (36 upd.)^*

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Official Debian package

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The package is enhanced by the following packages: multiqc

Please cite: Brian Bushnell, Jonathan Rood and Esther Singer: BBMerge – Accurate paired shotgun read merging via overlap. (PubMed,eprint) PLOS One (2017)

Registry entries: Bio.tools SciCrunch Bioconda

bcalm

??? missing short description for package bcalm :-(

https://github.com/GATB/bcalm

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package bcalm
Release	Version	Architectures
trixie	2.2.3-5	amd64,arm64,ppc64el,riscv64
bookworm	2.2.3-4	amd64,arm64,mips64el,ppc64el
bullseye	2.2.3-1	amd64,arm64,i386
forky	2.2.3-6	amd64,arm64,ppc64el,riscv64
sid	2.2.3-6	amd64,arm64,loong64,ppc64el,riscv64

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License: DFSG free

Official Debian package

Git

Please cite: Rayan Chikhi, Antoine Limasset and Paul Medvedev: Compacting de Bruijn graphs from sequencing data quickly and in low memory.. (eprint) Bioinformatics 32(12):208 (2016)

bcftools

??? missing short description for package bcftools :-(

https://samtools.github.io/bcftools/

Maintainer: Debian Med Packaging Team (Steffen Möller)

Versions of package bcftools
Release	Version	Architectures
bullseye	1.11-1	amd64,arm64,armhf,i386
sid	1.22-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.22-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.21-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.16-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el
upstream	1.23.1

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The package is enhanced by the following packages: multiqc

Please cite: Petr Danecek and Shane A. McCarthy: BCFtools/csq: Haplotype-aware variant consequences. (2016)

Registry entries: Bio.tools SciCrunch Bioconda

beads

??? missing short description for package beads :-(

http://pappso.inrae.fr/bioinfo/beads

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package beads
Release	Version	Architectures
trixie-proposed-updates	1.1.22-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.1.22+ds-1	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.1.22-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.1.22+ds-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.1.22-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	1.1.20-2	amd64,arm64,armhf,i386

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License: DFSG free

Official Debian package

Git

Please cite: Olivier Langella and Michel Zivy: A method based on bead flows for spot detection on 2-D gel images. (PubMed) Proteomics 8(23-24):4914-8 (2008)

beagle

??? missing short description for package beagle :-(

https://faculty.washington.edu/browning/beagle/beagle.html

Maintainer: Debian Med Packaging Team (Dylan Aïssi)

Versions of package beagle
Release	Version	Architectures
bullseye	5.1-200518+dfsg-1	all
trixie	241217-3	all
forky	250227-2	all
sid	250227-2	all
bookworm	220722-1	all

Popcon: 6 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: beagle-doc

Please cite: Sharon R. Browning and Brian L. Browning: Rapid and Accurate Haplotype Phasing and Missing-Data Inference for Whole-Genome Association Studies By Use of Localized Haplotype Clustering. (eprint) The American Journal of Human Genetics 81(5):1084-1097 (2007)

Registry entries: Bio.tools SciCrunch Bioconda

beast-mcmc

??? missing short description for package beast-mcmc :-(

http://beast.bio.ed.ac.uk/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package beast-mcmc
Release	Version	Architectures
bookworm	1.10.4+dfsg-5	all
bullseye	1.10.4+dfsg-2	all
trixie	1.10.4+dfsg-7	all
sid	1.10.4+dfsg-8	all
upstream	10.5.0

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Official Debian package

Git

The package is enhanced by the following packages: beast-mcmc-examples

Please cite: Alexei J Drummond and Andrew Rambaut: BEAST: Bayesian evolutionary analysis by sampling trees. (PubMed,eprint) BMC Evol Biol 8(7):214 (2007)

Registry entries: Bio.tools SciCrunch Bioconda

beast2-mcmc

??? missing short description for package beast2-mcmc :-(

https://www.beast2.org

Maintainer: Debian Med Packaging Team (Pierre Gruet)

Versions of package beast2-mcmc
Release	Version	Architectures
bookworm	2.7.3+dfsg-1	all
bullseye	2.6.3+dfsg-2	all
trixie	2.7.6+dfsg-1	all
sid	2.7.6+dfsg-1	all
upstream	2.7.8

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The package is enhanced by the following packages: beast2-mcmc-doc beast2-mcmc-examples

Please cite: Remco Bouckaert, Joseph Heled, Denise Kühnert, Tim Vaughan, Chieh-Hsi Wu, Dong Xie, Marc A. Suchard, Andrew Rambaut and Alexei J. Drummond: BEAST 2: A Software Platform for Bayesian Evolutionary Analysis. (PubMed,eprint) PLoS Comput Biol 10(4):e1003537 (2014)

Registry entries: Bio.tools SciCrunch Bioconda

bedops

??? missing short description for package bedops :-(

https://github.com/bedops/bedops

Maintainer: Debian Med Packaging Team (Steffen Moeller)

Versions of package bedops
Release	Version	Architectures
sid	2.4.42+dfsg-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2.4.39+dfsg1-2	amd64,arm64,armhf,i386
bookworm	2.4.41+dfsg-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	2.4.41+dfsg-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	2.4.42+dfsg-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 11 users (32 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Shane Neph, M. Scott Kuehn, Alex P. Reynolds, Eric Haugen, Robert E. Thurman, Audra K. Johnson, Eric Rynes, Matthew T. Maurano, Jeff Vierstra, Sean Thomas, Richard Sandstrom, Richard Humbert and John A. Stamatoyannopoulos: BEDOPS: high-performance genomic feature operations. (PubMed,eprint) 28(14):1919-1920 (2012)

Registry entries: Bio.tools SciCrunch Bioconda

bedtools

??? missing short description for package bedtools :-(

https://github.com/arq5x/bedtools2

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package bedtools
Release	Version	Architectures
bookworm	2.30.0+dfsg-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	2.31.1+dfsg-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	2.31.1+dfsg-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	2.31.1+dfsg-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2.30.0+dfsg-1	amd64,arm64,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

Popcon: 65 users (110 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Aaron R. Quinlan and Ira M. Hall: BEDTools: a flexible suite of utilities for comparing genomic features. (PubMed,eprint) Bioinformatics 26(6):841-842 (2010)

Registry entries: Bio.tools SciCrunch Bioconda

belvu

??? missing short description for package belvu :-(

https://www.sanger.ac.uk/science/tools/seqtools

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package belvu
Release	Version	Architectures
bullseye	4.44.1+dfsg-6	amd64,arm64,armhf,i386
sid	4.44.1+dfsg-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	4.44.1+dfsg-7.1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	4.44.1+dfsg-7	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

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License: DFSG free

Official Debian package

Git

Please cite: Gemma Barson and Ed Griffiths: SeqTools: visual tools for manual analysis of sequence alignments. (PubMed,eprint) BMC Research Notes 9:39 (2016)

Registry entries: Bio.tools SciCrunch

berkeley-express

??? missing short description for package berkeley-express :-(

http://bio.math.berkeley.edu/eXpress/index.html

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package berkeley-express
Release	Version	Architectures
bullseye	1.5.3+dfsg-1	amd64,arm64,armhf,i386
forky	1.5.3+dfsg-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.5.3+dfsg-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.5.3+dfsg-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.5.3+dfsg-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

Please cite: Adam Roberts and Lior Pachter: Streaming fragment assignment for real-time analysis of sequencing experiments. (PubMed) Nature Methods 10(1):71–73 (2013)

Registry entries: SciCrunch Bioconda

bifrost

??? missing short description for package bifrost :-(

https://github.com/pmelsted/bifrost

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package bifrost
Release	Version	Architectures
trixie	1.3.1-1	amd64,arm64,ppc64el,riscv64,s390x
sid	1.3.5-2	amd64,arm64,loong64,ppc64el,riscv64,s390x
forky	1.3.5-2	amd64,arm64,loong64,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

Please cite: Guillaume Holley and Páll Melsted: Bifrost – Highly parallel construction and indexing of colored and compacted de Bruijn graphs. (PubMed,eprint) bioRxiv 21(1):249 (2020)

Registry entries: Bio.tools Bioconda

bio-eagle

??? missing short description for package bio-eagle :-(

https://data.broadinstitute.org/alkesgroup/Eagle/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package bio-eagle
Release	Version	Architectures
sid	2.4.1-3	amd64,i386
forky	2.4.1-3	amd64,i386
trixie	2.4.1-3	amd64,i386
bookworm	2.4.1-3	amd64,i386
bullseye	2.4.1-3	amd64,i386

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: bio-eagle-examples

Please cite: Po-Ru Loh, Pier Francesco Palamara and Alkes L Price: Fast and accurate long-range phasing in a UK Biobank cohort. Nature Genetics (2016)

bio-rainbow

??? missing short description for package bio-rainbow :-(

http://sourceforge.net/projects/bio-rainbow/

Maintainer: Debian Med Packaging Team (Pranav Ballaney)

Versions of package bio-rainbow
Release	Version	Architectures
sid	2.0.4+dfsg-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	2.0.4+dfsg-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2.0.4+dfsg-2	amd64,arm64,armhf,i386
bookworm	2.0.4+dfsg-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	2.0.4+dfsg-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 6 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Zechen Chong, Jue Ruan and Chung-I. Wu: Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads.. (PubMed) Bioinformatics 28(21):2732-2737 (2012)

Registry entries: Bio.tools SciCrunch Bioconda

bio-tradis

??? missing short description for package bio-tradis :-(

https://github.com/sanger-pathogens/Bio-Tradis

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package bio-tradis
Release	Version	Architectures
trixie	1.4.5+dfsg2-2	all
bookworm	1.4.5+dfsg2-1	all
bullseye	1.4.5+dfsg2-1	all
forky	1.4.5+dfsg2-2	all
sid	1.4.5+dfsg2-2	all

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License: DFSG free

Official Debian package

Git

Please cite: Lars Barquist, Matthew Mayho, Carla Cummins, Amy K. Cain, Christine J. Boinett, Andrew J. Page, Gemma C. Langridge, Michael A. Quail, Jacqueline A. Keane and Julian Parkhill: The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries. (PubMed,eprint) Bioinformatics 32(7):1109-1111 (2016)

Registry entries: Bio.tools SciCrunch Bioconda

bio-vcf

??? missing short description for package bio-vcf :-(

https://github.com/vcflib/bio-vcf

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Popcon: 4 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

bioawk

??? missing short description for package bioawk :-(

https://github.com/lh3/bioawk

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package bioawk
Release	Version	Architectures
trixie	1.0-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.0-4+deb12u1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	1.0-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.0-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

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Git

Registry entries: Bioconda

biobambam2

??? missing short description for package biobambam2 :-(

https://gitlab.com/german.tischler/biobambam2

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package biobambam2
Release	Version	Architectures
bullseye	2.0.179+ds-1	amd64,arm64,i386
sid	2.0.185+ds-2	amd64,loong64,ppc64el,riscv64
bookworm	2.0.185+ds-1	amd64,arm64,i386,ppc64el
trixie	2.0.185+ds-2	amd64,ppc64el,riscv64
forky	2.0.185+ds-2	amd64,loong64,ppc64el,riscv64
upstream	2.0.185-release-20221211202123

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: multiqc

Please cite: German Tischler and Steven Leonard: biobambam: tools for read pair collation based algorithms on BAM files. (eprint) Source Code Biol Med. 9:13 (2014)

Registry entries: Bio.tools SciCrunch Bioconda

biosyntax

??? missing short description for package biosyntax :-(

https://biosyntax.org/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package biosyntax
Release	Version	Architectures
trixie	1.0.0b-6	all
bookworm	1.0.0b-4	all
forky	1.0.0b-6	all
bullseye	1.0.0b-2	all
sid	1.0.0b-6	all

Popcon: 0 users (0 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Artem Babaian, Anicet Ebou, Alyssa Fegen, Ho Yin Jeffrey Kam, German E Novakovsky, Jasper Wong, Dylan Aïssi and Li Yao: bioSyntax: syntax highlighting for computational biology. BMC Bioinformatics 19(303) (2018)

Registry entries: Bio.tools SciCrunch

bitseq

??? missing short description for package bitseq :-(

https://github.com/BitSeq/BitSeq

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package bitseq
Release	Version	Architectures
bullseye	0.7.5+dfsg-5	amd64,arm64,armhf,i386
forky	0.7.5+dfsg2-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	0.7.5+dfsg-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	0.7.5+dfsg-6	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	0.7.5+dfsg2-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

Please cite: James Hensman, Panagiotis Papastamoulis, Peter Glaus, Antti Honkela and Magnus Rattray: Fast and accurate approximate inference of transcript expression from RNA-seq data. (PubMed,eprint) Bioinformatics 31(24):3881-9 (2015)

Registry entries: Bio.tools SciCrunch

blasr

??? missing short description for package blasr :-(

https://github.com/PacificBiosciences/blasr

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package blasr
Release	Version	Architectures
bookworm	5.3.5+dfsg-6	amd64,arm64,mips64el,ppc64el
trixie	5.3.5+dfsg-7	amd64,arm64,ppc64el,riscv64
bullseye	5.3.3+dfsg-5	amd64,arm64
sid	5.3.5+dfsg-8	amd64,arm64,loong64,ppc64el,riscv64
forky	5.3.5+dfsg-8	amd64,arm64,ppc64el,riscv64

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License: DFSG free

Official Debian package

Git

Please cite: Mark J Chaisson and Glenn Tesler: Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. (PubMed) BMC Bioinformatics 13(238) (2012)

Registry entries: Bio.tools SciCrunch Bioconda

blixem

??? missing short description for package blixem :-(

https://www.sanger.ac.uk/science/tools/seqtools

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package blixem
Release	Version	Architectures
trixie	4.44.1+dfsg-7.1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	4.44.1+dfsg-7	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	4.44.1+dfsg-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	4.44.1+dfsg-6	amd64,arm64,armhf,i386

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License: DFSG free

Official Debian package

Git

Please cite: Gemma Barson and Ed Griffiths: SeqTools: visual tools for manual analysis of sequence alignments. (PubMed,eprint) BMC Research Notes 9:39 (2016)

Registry entries: Bio.tools SciCrunch

bolt-lmm

??? missing short description for package bolt-lmm :-(

https://data.broadinstitute.org/alkesgroup/BOLT-LMM/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package bolt-lmm
Release	Version	Architectures
forky	2.4.1+dfsg-2	amd64,i386,ppc64el
trixie	2.4.1+dfsg-2	amd64,i386,ppc64el
bookworm	2.4.0+dfsg-1	amd64,i386,ppc64el
bullseye	2.3.4+dfsg-3	amd64,i386
sid	2.4.1+dfsg-2	amd64,i386,ppc64el
upstream	2.5

Popcon: 4 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: bolt-lmm-example

Please cite: Po-Ru Loh, George Tucker, Brendan K Bulik-Sullivan, Bjarni J Vilhjálmsson, Hilary K Finucane, Rany M Salem, Daniel I Chasman, Paul M Ridker, Benjamin M Neale, Bonnie Berger, Nick Patterson and Alkes L Price: Efficient Bayesian mixed-model analysis increases association power in large cohorts. Nature Genetics (2015)

bowtie

??? missing short description for package bowtie :-(

https://bowtie-bio.sourceforge.net/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package bowtie
Release	Version	Architectures
sid	1.3.1-3	amd64,arm64,loong64,ppc64el,riscv64,s390x
forky	1.3.1-3	amd64,arm64,loong64,ppc64el,riscv64,s390x
trixie	1.3.1-3	amd64,arm64,ppc64el,riscv64,s390x
bookworm	1.3.1-1	amd64,arm64,mips64el,ppc64el,s390x
bullseye	1.3.0+dfsg1-1	amd64,arm64

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

Popcon: 19 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: bowtie-examples multiqc

Please cite: Ben Langmead, Cole Trapnell, Mihai Pop and Steven L Salzberg: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. (eprint) Genome Biology 10:R25 (2009)

Registry entries: Bio.tools SciCrunch Bioconda

Topics: Genomics

bowtie2

??? missing short description for package bowtie2 :-(

https://bowtie-bio.sourceforge.net/bowtie2

Maintainer: Debian Med Packaging Team (Steffen Moeller)

Versions of package bowtie2
Release	Version	Architectures
forky	2.5.5-1	amd64,arm64,loong64,ppc64el,riscv64
bookworm	2.5.0-3	amd64,arm64,mips64el,ppc64el
trixie	2.5.4-1	amd64,arm64,ppc64el,riscv64
sid	2.5.5-1	amd64,arm64,loong64,ppc64el,riscv64
bullseye	2.4.2-2	amd64,arm64

Popcon: 24 users (46 upd.)^*

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: bowtie2-examples multiqc

Please cite: Ben Langmead and Steven L Salzberg: Fast gapped-read alignment with Bowtie 2. (PubMed) Nature Methods 9:357–359 (2012)

Registry entries: Bio.tools SciCrunch Bioconda

Topics: Genomics

boxshade

??? missing short description for package boxshade :-(

http://www.ch.embnet.org/software/BOX_form.html

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package boxshade
Release	Version	Architectures
trixie	3.3.1-14	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	3.3.1-14	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	3.3.1-14	amd64,arm64,armhf,i386
bookworm	3.3.1-14	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	3.3.1-14	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Debtags of package boxshade:
biology	format:aln, nuceleic-acids, peptidic
field	biology, biology:bioinformatics
interface	commandline
role	program
scope	utility
use	typesetting
works-with-format	html, plaintext, postscript, tex

Popcon: 10 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools SciCrunch

bppphyview

??? missing short description for package bppphyview :-(

http://biopp.univ-montp2.fr/wiki/index.php/Main_Page

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package bppphyview
Release	Version	Architectures
sid	0.6.1-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	0.6.1-2	amd64,arm64,armhf,i386
bookworm	0.6.1-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	0.6.1-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	0.6.1-6	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
upstream	0.7.0

Popcon: 5 users (35 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

bppsuite

??? missing short description for package bppsuite :-(

http://biopp.univ-montp2.fr/wiki/index.php/Main_Page

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package bppsuite
Release	Version	Architectures
trixie	2.4.1-7	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	2.4.1-3	amd64,arm64,armhf,i386
bookworm	2.4.1-6	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	2.4.1-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	2.4.1-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

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The package is enhanced by the following packages: bppsuite-examples

brig

??? missing short description for package brig :-(

http://sourceforge.net/projects/brig/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package brig
Release	Version	Architectures
bullseye	0.95+dfsg-3	amd64,arm64,armhf,i386
bookworm	0.95+dfsg-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	0.95+dfsg-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	0.95+dfsg-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	0.95+dfsg-3	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x

Popcon: 3 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Nabil-Fareed Alikhan, Nicola K Petty, Nouri L Ben Zakour and Scott A Beatson: BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. (PubMed,eprint) BMC Genomics 12:402 (2011)

Registry entries: Bio.tools SciCrunch

btllib-tools

??? missing short description for package btllib-tools :-(

https://github.com/bcgsc/btllib

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package btllib-tools
Release	Version	Architectures
trixie	1.7.5+dfsg-2	amd64,arm64,ppc64el,riscv64,s390x
sid	1.7.5+dfsg-2	amd64,arm64,loong64,ppc64el,riscv64,s390x
forky	1.7.5+dfsg-2	amd64,arm64,loong64,ppc64el,riscv64,s390x
bookworm	1.4.10+dfsg-1	amd64,arm64,mips64el,ppc64el
upstream	1.7.8

Popcon: 5 users (34 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: Vladimir Nikolić, Parham Kazemi, Lauren Coombe, Johnathan Wong, Amirhossein Afshinfard, Justin Chu, René L. Warren and Inanç Birol: btllib: A C++ library with Python interface for efficient genomic sequence processing. (eprint) Journal of Open Source Software 7(79) (2022)

Registry entries: Bioconda

busco

??? missing short description for package busco :-(

https://gitlab.com/ezlab/busco

Maintainer: Debian Med Packaging Team (Alexandre Detiste)

Versions of package busco
Release	Version	Architectures
bookworm	5.4.4-1	amd64,i386
sid	5.5.0-4	amd64,arm64,i386
bullseye	5.0.0-1	all
trixie	5.5.0-3	amd64,arm64,i386
forky	5.5.0-4	amd64,arm64,i386
upstream	6.0.0

Popcon: 9 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: multiqc

Please cite: Mathieu Seppey, Mosè Manni and Evgeny M. Zdobnov: BUSCO: Assessing Genome Assembly and Annotation Completeness. (PubMed) Methods Mol Biol. 1962:227-245 (2019)

Registry entries: Bio.tools Bioconda

bustools

??? missing short description for package bustools :-(

https://bustools.github.io/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package bustools
Release	Version	Architectures
trixie	0.43.2+dfsg-1	amd64,arm64,ppc64el,riscv64,s390x
bookworm	0.42.0+dfsg-1	amd64,arm64,mips64el,ppc64el,s390x
sid	0.45.1+dfsg-1	amd64,arm64,loong64,ppc64el,riscv64,s390x
bullseye	0.40.0-4	amd64,arm64
forky	0.45.1+dfsg-1	amd64,arm64,loong64,ppc64el,riscv64,s390x

Popcon: 5 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Páll Melsted, A. Sina Booeshaghi, Fan Gao, Eduardo Beltrame, Lambda Lu, Kristján Eldjárn Hjorleifsson, Jase Gehring and Lior Pachter: Modular and efficient pre-processing of single-cell RNA-seq.. BioRxiv :673285 (2019)

Registry entries: Bio.tools Bioconda

bwa

??? missing short description for package bwa :-(

https://bio-bwa.sourceforge.net/

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package bwa
Release	Version	Architectures
sid	0.7.19-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	0.7.17-7	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	0.7.18-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	0.7.19-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	0.7.17-6	amd64,arm64,armhf,i386

Debtags of package bwa:
biology	nuceleic-acids, peptidic
field	biology, biology:bioinformatics
interface	commandline, text-mode
role	program
use	analysing, comparing

Popcon: 20 users (35 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Heng Li and Richard Durbin: Fast and accurate short read alignment with Burrows-Wheeler transform. (PubMed,eprint) Bioinformatics 25(14):1754-1760 (2009)

Registry entries: Bio.tools SciCrunch Bioconda

canu

??? missing short description for package canu :-(

https://canu.readthedocs.org/en/latest/

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package canu
Release	Version	Architectures
bookworm	2.0+dfsg-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	2.2+dfsg-5	amd64,arm64,loong64,ppc64el,riscv64,s390x
bullseye	2.0+dfsg-1	amd64,arm64,armhf,i386
upstream	2.3

Popcon: 1 users (0 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: Sergey Koren, Brian P. Walenz, Konstantin Berlin, Jason R. Miller and Adam M. Phillippy: Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.. Genome Res. (2017)

Registry entries: Bio.tools SciCrunch Bioconda

Remark of Debian Med team: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)

cassiopee

??? missing short description for package cassiopee :-(

https://github.com/osallou/cassiopee-c

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package cassiopee
Release	Version	Architectures
forky	1.0.9-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.0.9-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.0.9-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.0.9-3	amd64,arm64,armhf,i386
trixie	1.0.9-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 6 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: SciCrunch Bioconda

cat-bat

??? missing short description for package cat-bat :-(

https://github.com/dutilh/CAT

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package cat-bat
Release	Version	Architectures
sid	6.0.1-1	amd64,arm64,loong64,ppc64el,riscv64,s390x
forky	6.0.1-1	amd64,arm64,loong64,ppc64el,riscv64,s390x
bullseye	5.2.2-1	amd64,arm64
trixie	5.3-2	amd64,arm64,ppc64el,riscv64,s390x
bookworm	5.2.3-2	amd64,arm64,ppc64el,s390x

Popcon: 3 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: F. A. Bastiaan von Meijenfeldt, Ksenia Arkhipova, Diego D. Cambuy, Felipe H. Coutinho and Bas E. Dutilh: Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT. (PubMed,eprint) Genome Biology 20(1):217 (2019)

Registry entries: Bioconda

cct

??? missing short description for package cct :-(

http://stothard.afns.ualberta.ca/downloads/CCT/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Popcon: 4 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Jason R Grant, Adriano S Arantes and Paul Stothard: Comparing thousands of circular genomes using the CGView Comparison Tool. (PubMed,eprint) BMC Genomics 13:202 (2012)

cd-hit

??? missing short description for package cd-hit :-(

http://weizhongli-lab.org/cd-hit/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package cd-hit
Release	Version	Architectures
sid	4.8.1-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	4.8.1-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	4.8.1-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	4.8.1-3	amd64,arm64,armhf,i386
trixie	4.8.1-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 10 users (36 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Weizhong Li and Adam Godzik: Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.. (PubMed,eprint) Bioinformatics 22 (2006)

Registry entries: Bio.tools SciCrunch Bioconda

Topics: Genomics

cdbfasta

??? missing short description for package cdbfasta :-(

https://github.com/gpertea/cdbfasta

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package cdbfasta
Release	Version	Architectures
bookworm	1.00+git20181005.014498c+dfsg-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.00+git20230710.da8f5ba+dfsg-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.00+git20230710.da8f5ba+dfsg-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.00+git20230710.da8f5ba+dfsg-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	1.00+git20181005.014498c+dfsg-2	amd64,arm64,armhf,i386

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License: DFSG free

Official Debian package

Git

Registry entries: SciCrunch

centrifuge

??? missing short description for package centrifuge :-(

https://ccb.jhu.edu/software/centrifuge/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package centrifuge
Release	Version	Architectures
sid	1.0.4.2-1	amd64,arm64,loong64,ppc64el,riscv64
forky	1.0.4.2-1	amd64,arm64,loong64,ppc64el,riscv64
trixie	1.0.4.2-1	amd64,arm64,ppc64el,riscv64
bullseye	1.0.3-8	amd64,arm64,armhf,i386
bookworm	1.0.3-11	amd64,arm64,armel,armhf,i386,mips64el,ppc64el

Popcon: 7 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Daehwan Kim, Li Song, Florian P. Breitwieser and Steven L. Salzberg: Centrifuge: rapid and sensitive classification of metagenomic sequences. (PubMed,eprint) Genome Research 26(12):1721-1729 (2016)

Registry entries: Bio.tools Bioconda

cgview

??? missing short description for package cgview :-(

http://wishart.biology.ualberta.ca/cgview/

Maintainer: Debian Med Packaging Team (Pierre Gruet)

Versions of package cgview
Release	Version	Architectures
sid	0.0.20100111-8	all
forky	0.0.20100111-8	all
bookworm	0.0.20100111-7	all
bullseye	0.0.20100111-7	all
trixie	0.0.20100111-7	all

Popcon: 4 users (39 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Paul Stothard and David S. Wishart: Circular genome visualization and exploration using CGView. (PubMed,eprint) Bioinformatics 21(4):537-539 (2004)

Registry entries: Bio.tools SciCrunch Bioconda

changeo

??? missing short description for package changeo :-(

https://changeo.readthedocs.io

Maintainer: Debian Med Packaging Team (Alexandre Detiste)

Versions of package changeo
Release	Version	Architectures
trixie	1.3.0-3	all
bullseye	1.0.2-1	all
bookworm	1.3.0-1	all
forky	1.3.0-4	all
sid	1.3.0-4	all
upstream	1.3.4

Popcon: 9 users (34 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: Namita T. Gupta, Jason A. Vander Heiden, Mohamed Uduman, Daniel Gadala-Maria, Gur Yaari and Steven H. Kleinstein: Link to publication (PubMed,eprint) Bioinformatics 31(20):3356-3358 (2015)

Registry entries: Bioconda

chimeraslayer

??? missing short description for package chimeraslayer :-(

https://microbiomeutil.sourceforge.net/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package chimeraslayer
Release	Version	Architectures
sid	20101212+dfsg1-6	all
bookworm	20101212+dfsg1-5	all
forky	20101212+dfsg1-6	all
bullseye	20101212+dfsg1-4	all
trixie	20101212+dfsg1-6	all

Popcon: 5 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: microbiomeutil-data

Please cite: Brian J. Haas, Dirk Gevers, Ashlee M. Earl, Mike Feldgarden, Doyle V. Ward, Georgia Giannoukos, Dawn Ciulla, Diana Tabbaa, Sarah K. Highlander, Erica Sodergren, Barbara Methé, Todd Z. DeSantis, The Human Microbiome Consortium, Joseph F. Petrosino, Rob Knight and Bruce W. Birren: Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. (PubMed,eprint) Genome Research 21(3):494-504 (2011)

Registry entries: SciCrunch

chromhmm

??? missing short description for package chromhmm :-(

https://compbio.mit.edu/ChromHMM/

Maintainer: Debian Med Packaging Team (Dylan Aïssi)

Versions of package chromhmm
Release	Version	Architectures
trixie	1.26+dfsg-3	all
bullseye	1.21+dfsg-1	all
forky	1.27+dfsg-1	all
bookworm	1.24+dfsg-1	all
sid	1.27+dfsg-1	all

Popcon: 5 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: chromhmm-example

Please cite: Jason Ernst and Manolis Kellis: ChromHMM: automating chromatin-state discovery and characterization. (eprint) Nature Methods 9(3):215-216 (2012)

Registry entries: Bio.tools Bioconda

chromimpute

??? missing short description for package chromimpute :-(

https://www.biolchem.ucla.edu/labs/ernst/ChromImpute/

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package chromimpute
Release	Version	Architectures
bookworm	1.0.3+dfsg-4	all
trixie	1.0.3+dfsg-5	all
bullseye	1.0.3+dfsg-2	all
forky	1.0.3+dfsg-6	all
sid	1.0.3+dfsg-6	all

Popcon: 4 users (36 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Jason Ernst and Manolis Kellis: Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues. (eprint) Nature Biotechnology 33(4):364-376 (2015)

cif-tools

??? missing short description for package cif-tools :-(

https://github.com/PDB-REDO/cif-tools

Maintainer: Debian Med Packaging Team (Maarten L. Hekkelman)

Versions of package cif-tools
Release	Version	Architectures
bullseye	1.0.0-3	amd64,arm64,armhf,i386
sid	2.0.0-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.0.7-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	1.0.13-1	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
trixie	1.0.12-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 8 users (32 upd.)^*

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License: DFSG free

Official Debian package

Git

circlator

??? missing short description for package circlator :-(

https://sanger-pathogens.github.io/circlator/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Popcon: 0 users (0 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Martin Hunt, Nishadi De Silva, Thomas D. Otto, Julian Parkhill, Jacqueline A. Keane and Simon R. Harris: Circlator: automated circularization of genome assemblies using long sequencing reads. (PubMed) Genome Biology 29(16):294 (2015)

Registry entries: SciCrunch Bioconda

circos

??? missing short description for package circos :-(

https://circos.ca/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package circos
Release	Version	Architectures
trixie	0.69.9+dfsg-2	all
forky	0.69.9+dfsg-3	all
bookworm	0.69.9+dfsg-2	all
sid	0.69.9+dfsg-3	all
bullseye	0.69.9+dfsg-2	all

Popcon: 6 users (35 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Martin I Krzywinski, Jacqueline E Schein, Inanc Birol, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J Jones and Marco A Marra: Circos: An information aesthetic for comparative genomics. (PubMed,eprint) Genome Research 19(9):1639-45 (2009)

Registry entries: Bio.tools SciCrunch Bioconda

clearcut

??? missing short description for package clearcut :-(

https://github.com/sheneman/clearcut

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package clearcut
Release	Version	Architectures
trixie	1.0.9+git20211013.b799afe-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.0.9+git20211013.b799afe-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.0.9+git20211013.b799afe-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.0.9-6	amd64,arm64,armhf,i386
bookworm	1.0.9+git20211013.b799afe-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 6 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Jason Evans, Luke Sheneman and James A. Foster: Relaxed Neighbor-Joining: A Fast Distance-Based Phylogenetic Tree Construction Method. (PubMed) J. Mol. Evol. 62(6):785-792 (2006)

Registry entries: SciCrunch Bioconda

clonalframe

??? missing short description for package clonalframe :-(

http://www.xavierdidelot.xtreemhost.com/clonalframe.htm

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package clonalframe
Release	Version	Architectures
sid	1.2-11	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.2-11	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.2-11	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.2-11	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.2-10	amd64,arm64,armhf,i386

Popcon: 5 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Xavier Didelot and Daniel Falush: Inference of Bacterial Microevolution Using Multilocus Sequence Data. (PubMed,eprint) Genetics Advance 175:1251-1266 (2006)

Registry entries: SciCrunch

clonalframeml

??? missing short description for package clonalframeml :-(

https://github.com/xavierdidelot/ClonalFrameML

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package clonalframeml
Release	Version	Architectures
trixie	1.13-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.13-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.13-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.12-1	amd64,arm64,armhf,i386
bookworm	1.12-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 4 users (35 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Xavier Didelot and Daniel J. Wilson: ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes. (PubMed,eprint) PLoS Comput Biology 11(2):e1004041 (2015)

Registry entries: Bioconda

clonalorigin

??? missing short description for package clonalorigin :-(

https://github.com/xavierdidelot/clonalorigin

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package clonalorigin
Release	Version	Architectures
forky	1.0-9	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.0-8	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	1.0-4	amd64,arm64,armhf,i386
bookworm	1.0-6	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.0-9	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 5 users (35 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Xavier Didelot, Daniel Lawson, Aaron Darling and Daniel Falush: Inference of Homologous Recombination in Bacteria Using Whole-Genome Sequences. (PubMed,eprint) Genetics 186(4):1435-1449 (2010)

Registry entries: Bio.tools SciCrunch

clustalo

??? missing short description for package clustalo :-(

http://www.clustal.org/omega/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package clustalo
Release	Version	Architectures
forky	1.2.4-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.2.4-8	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.2.4-7	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.2.4-7	amd64,arm64,armhf,i386
sid	1.2.4-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 23 users (41 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

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)

Registry entries: Bio.tools SciCrunch Bioconda

Topics: Sequence analysis

clustalw

??? missing short description for package clustalw :-(

http://www.clustal.org/clustal2/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package clustalw
Release	Version	Architectures
trixie	2.1+lgpl-7	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	2.1+lgpl-7	amd64,arm64,armhf,i386
bookworm	2.1+lgpl-7	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	2.1+lgpl-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	2.1+lgpl-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,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

Popcon: 17 users (37 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

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)

Registry entries: Bio.tools SciCrunch Bioconda

Topics: Sequence analysis

clustalx

??? missing short description for package clustalx :-(

http://www.clustal.org/clustal2/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package clustalx
Release	Version	Architectures
bullseye	2.1+lgpl-9	amd64,arm64,armhf,i386
bookworm	2.1+lgpl-9	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	2.1+lgpl-9	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	2.1+lgpl-9	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	2.1+lgpl-9	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Debtags of package clustalx:
biology	format:aln, nuceleic-acids, peptidic
field	biology, biology:bioinformatics
interface	x11
role	program
scope	utility
uitoolkit	motif
use	analysing, comparing, viewing
works-with-format	plaintext
x11	application

Popcon: 11 users (36 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

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)

Registry entries: Bio.tools SciCrunch

Topics: Sequence analysis

cnvkit

??? missing short description for package cnvkit :-(

https://cnvkit.readthedocs.org

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package cnvkit
Release	Version	Architectures
bullseye	0.9.8-1	amd64,arm64
trixie	0.9.12-1	all
sid	0.9.12-1	all
bookworm	0.9.9-2	amd64,arm64,ppc64el
upstream	0.9.13

Popcon: 14 users (32 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: Eric Talevich, A. Hunter Shain, Thomas Botton and Boris C. Bastian: CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing. (PubMed,eprint) PLOS 12(4):e1004873 (2016)

Registry entries: Bio.tools Bioconda

codonw

??? missing short description for package codonw :-(

https://codonw.sourceforge.net

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package codonw
Release	Version	Architectures
bookworm	1.4.4-7	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.4.4-8	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.4.4-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.4.4-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.4.4-6	amd64,arm64,armhf,i386

Popcon: 6 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Paul M. Sharp, Elizabeth Bailes, Russell J. Grocock, John F. Peden and R. Elizabeth Sockett: Variation in the strength of selected codon usage bias among bacteria.. (PubMed,eprint) Nucleic Acids Research 33(4):1141-1153 (2005)

Registry entries: Bioconda

Topics: Sequence composition, complexity and repeats

comet-ms

??? missing short description for package comet-ms :-(

http://comet-ms.sourceforge.net

Maintainer: The Debichem Group (Sebastian Ramacher)

Versions of package comet-ms
Release	Version	Architectures
forky	2019015+cleaned1-4.1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	2019015+cleaned1-4.1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	2019015+cleaned1-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	2019015+cleaned1-3	amd64,arm64,armhf,i386
sid	2019015+cleaned1-4.1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
upstream	2021010

Popcon: 5 users (34 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: Jimmy K. Eng, Tahmina A. Jahan and Michael R. Hoopmann: Comet: an open source tandem mass spectrometry sequence database search tool. (PubMed) Proteomics 13(1) (2012)

concavity

??? missing short description for package concavity :-(

https://compbio.cs.princeton.edu/concavity/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package concavity
Release	Version	Architectures
bullseye	0.1+dfsg.1-5	amd64,arm64,armhf,i386
sid	0.1+dfsg.1-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	0.1+dfsg.1-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	0.1+dfsg.1-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	0.1+dfsg.1-5	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 5 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: conservation-code

Please cite: John A. Capra, Roman A. Laskowski, Janet M. Thornton, Mona Singh and Thomas A. Funkhouser: Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure. (PubMed) PLoS Computational Biology 5(12):e1000585 (2009)

Registry entries: SciCrunch

conservation-code

??? missing short description for package conservation-code :-(

https://compbio.cs.princeton.edu/conservation/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package conservation-code
Release	Version	Architectures
bookworm	20110309.0-8	all
bullseye	20110309.0-8	all
sid	20110309.0-8	all
forky	20110309.0-8	all
trixie	20110309.0-8	all

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License: DFSG free

Official Debian package

Git

Please cite: John A. Capra and Mona Singh: Predicting functionally important residues from sequence conservation. (PubMed) Bioinformatics 23(15):1875-82 (2007)

coot

??? missing short description for package coot :-(

https://github.com/pemsley/coot

Maintainer: Debian Science Maintainers (Andrius Merkys)

Versions of package coot
Release	Version	Architectures
sid	1.1.18+dfsg-5	amd64,arm64,loong64,ppc64el,riscv64
forky	1.1.18+dfsg-5	amd64,arm64,ppc64el,riscv64
trixie	1.1.15+dfsg-1	amd64,arm64,ppc64el,riscv64
upstream	1.2

Popcon: 84 users (20 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: P. Emsley, B. Lohkamp, W. G. Scott and K. Cowtan: Features and development of Coot. (eprint) Acta Crystallographica Section D 66(4):486-501 (2010)

covtobed

??? missing short description for package covtobed :-(

https://github.com/telatin/covtobed

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package covtobed
Release	Version	Architectures
bullseye	1.2.0+dfsg-1	amd64,arm64,armhf,i386
forky	1.3.5+dfsg-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.3.5+dfsg-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.3.5+dfsg-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.3.5+dfsg-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
upstream	1.4.0

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License: DFSG free

Official Debian package

Git

Please cite: Giovanni Birolo and Andrea Telatin: covtobed: a simple and fast tool to extract coverage tracks from BAM files. Journal of Open Source Software 5(47):2119 (2020)

Registry entries: Bioconda

crac

??? missing short description for package crac :-(

https://crac.gforge.inria.fr/

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package crac
Release	Version	Architectures
sid	2.5.2+dfsg-7	amd64,arm64,loong64,ppc64el,riscv64
trixie	2.5.2+dfsg-6	amd64,arm64,ppc64el,riscv64
bullseye	2.5.2+dfsg-4	amd64,arm64,armhf,i386
forky	2.5.2+dfsg-7	amd64,arm64,loong64,ppc64el,riscv64
bookworm	2.5.2+dfsg-5	amd64,arm64,armel,armhf,i386,mips64el,ppc64el

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License: DFSG free

Official Debian package

Git

Please cite: Eliseos J. Mucaki, Natasha G. Caminsky, Ami M. Perri, Ruipeng Lu, Alain Laederach, Matthew Halvorsen, Joan H. M. Knoll and Peter K. Rogan: A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer. (PubMed) BMS Medical Genomics 9:19 (2016)

Registry entries: Bio.tools SciCrunch

csb

??? missing short description for package csb :-(

https://github.com/csb-toolbox/CSB

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package csb
Release	Version	Architectures
bookworm	1.2.5+dfsg-8	all
sid	1.2.5+dfsg-10	all
forky	1.2.5+dfsg-10	all
trixie	1.2.5+dfsg-10	all
bullseye	1.2.5+dfsg-5	all

Popcon: 11 users (32 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: SciCrunch Bioconda

ctffind

??? missing short description for package ctffind :-(

https://grigoriefflab.umassmed.edu/ctffind4

Maintainer: Debian Med Packaging Team (Alex Myczko)

Versions of package ctffind
Release	Version	Architectures
trixie	4.1.14-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	4.1.14-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	4.1.14-3	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
upstream	5.0.2

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License: DFSG free

Official Debian package

Git

Please cite: Alexis Rohou and Nikolaus Grigorieff: CTFFIND4: Fast and accurate defocus estimation from electron micrographs. (PubMed) Journal of Structural Biology 192(2):216-221 (2015)

Registry entries: SciCrunch

cutadapt

??? missing short description for package cutadapt :-(

https://cutadapt.readthedocs.io/

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package cutadapt
Release	Version	Architectures
sid	4.7-2	all
trixie	4.7-2	all
forky	4.7-2	all
bullseye	3.2-2	all
bookworm	4.2-1	all
upstream	5.2

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Official Debian package

Git

The package is enhanced by the following packages: multiqc

Please cite: Marcel Martin: Cutadapt removes adapter sequences from high-throughput sequencing reads. (eprint) EMBnet.journal 17(1):10-12 (2015)

Registry entries: Bio.tools SciCrunch Bioconda

cutesv

??? missing short description for package cutesv :-(

https://github.com/tjiangHIT/cuteSV

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package cutesv
Release	Version	Architectures
bookworm	2.0.2-1	all
trixie	2.1.1-1	all
forky	2.1.1-1	all
sid	2.1.1-1	all
upstream	2.1.3

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License: DFSG free

Official Debian package

Git

Please cite: Tao Jiang, Yongzhuang Liu, Yue Jiang, Junyi Li, Yan Gao, Zhe Cui, Yadong Liu, Bo Liu and Yadong Wang: Long-read-based human genomic structural variation detection with cuteSV. (PubMed,eprint) Genome Biology 21(1):189 (2020)

Registry entries: Bio.tools Bioconda

daligner

??? missing short description for package daligner :-(

https://dazzlerblog.wordpress.com

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package daligner
Release	Version	Architectures
sid	1.0+git20240119.335105d-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.0+git20240119.335105d-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.0+git20240119.335105d-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.0+git20221215.bd26967-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.0+git20200727.ed40ce5-3	amd64,arm64,armhf,i386

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License: DFSG free

Official Debian package

Git

Please cite: Gene Myers: Efficient Local Alignment Discovery amongst Noisy Long Reads. 8701:52-67 (2014)

Registry entries: SciCrunch Bioconda

damapper

??? missing short description for package damapper :-(

https://github.com/thegenemyers/DAMAPPER

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package damapper
Release	Version	Architectures
forky	0.0+git20240314.b025cf9-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	0.0+git20200322.b2c9d7f-3	amd64,arm64,armhf,i386
trixie	0.0+git20240314.b025cf9-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	0.0+git20210330.ab45103-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	0.0+git20240314.b025cf9-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

datamash

??? missing short description for package datamash :-(

https://savannah.gnu.org/projects/datamash/

Maintainer: Debian Science Maintainers (Dima Kogan)

Versions of package datamash
Release	Version	Architectures
bullseye	1.7-2	amd64,arm64,armhf,i386
sid	1.9-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.7-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.9-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.9-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

Registry entries: SciCrunch

dawg

??? missing short description for package dawg :-(

https://github.com/reedacartwright/dawg

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package dawg
Release	Version	Architectures
forky	1.2-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.2-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	1.2-3	amd64,arm64,armhf,i386
sid	1.2-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.2-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 5 users (32 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Reed A. Cartwright: DNA assembly with gaps (Dawg): simulating sequence evolution. (PubMed,eprint) Bioinformatics 21(Suppl 3):iii31-iii38 (2005)

Registry entries: Bioconda

dazzdb

??? missing short description for package dazzdb :-(

https://github.com/thegenemyers/DAZZ_DB

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package dazzdb
Release	Version	Architectures
forky	1.0+git20250217.a3eefd4-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.0+git20250217.a3eefd4-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.0+git20221215.aad3a46-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.0+git20201103.8d98c37-1+deb11u1	amd64,arm64,armhf,i386
trixie	1.0+git20250217.a3eefd4-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 10 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

deblur

??? missing short description for package deblur :-(

https://github.com/biocore/deblur

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Popcon: 8 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

deepnano

??? missing short description for package deepnano :-(

https://bitbucket.org/vboza/deepnano

Maintainer: Debian Med Packaging Team (Thomas Goirand)

Popcon: 0 users (0 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Vladimír Boža, Broňa Brejová and Tomáš Vinař: DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads. PLOS one (2017)

Remark of Debian Med team: There is no intend to keep continue the existing packaging since

the program nanocall seems to serve the intended purpose better

delly

??? missing short description for package delly :-(

https://github.com/dellytools/delly

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package delly
Release	Version	Architectures
trixie	1.1.8-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	0.8.7-1	amd64,arm64,armhf,i386
bookworm	1.1.6-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.7.2-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.7.2-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
upstream	1.7.3

Popcon: 6 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Tobias Rausch, Thomas Zichner, Andreas Schlattl, Adrian M. Stuetz, Vladimir Benes and Jan O. Korbel: DELLY: structural variant discovery by integrated paired-end and split-read analysis.. Bioinformatics 28:i333-i339 (2012)

Registry entries: Bio.tools SciCrunch Bioconda

density-fitness

??? missing short description for package density-fitness :-(

https://github.com/PDB-REDO/density-fitness

Maintainer: Debian Med Packaging Team (Maarten L. Hekkelman)

Versions of package density-fitness
Release	Version	Architectures
trixie	1.1.3-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.0.8-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.2.1-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.0.0-2	amd64,arm64,armhf,i386
forky	1.2.0-2	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x

Popcon: 6 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: I. J. Tickle: Statistical quality indicators for electron-density maps. Acta Cryst. (D68):454-467 (2012)

dextractor

??? missing short description for package dextractor :-(

https://github.com/thegenemyers/DEXTRACTOR

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package dextractor
Release	Version	Architectures
forky	1.0-7	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
trixie	1.0-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	1.0-4	amd64,arm64,armhf,i386
bookworm	1.0-6	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.0-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 7 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

dialign

??? missing short description for package dialign :-(

https://dialign.gobics.de/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package dialign
Release	Version	Architectures
sid	2.2.1-13	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	2.2.1-13	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	2.2.1-11	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	2.2.1-11	amd64,arm64,armhf,i386
forky	2.2.1-13	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,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

Popcon: 12 users (38 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Burkhard Morgenstern: DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. (PubMed,eprint) Bioinformatics 15(3):211-218 (1999)

Registry entries: Bio.tools SciCrunch Bioconda

dialign-tx

??? missing short description for package dialign-tx :-(

https://dialign-tx.gobics.de/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package dialign-tx
Release	Version	Architectures
bookworm	1.0.2-14	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.0.2-15	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.0.2-15	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.0.2-15	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.0.2-13	amd64,arm64,armhf,i386

Popcon: 11 users (36 upd.)^*

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: dialign-tx-data

Please cite: Amarendran R. Subramanian, Michael Kaufmann and Burkhard Morgenstern: DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment. (PubMed) Algorithms for Molecular Biology 3(1):6 (2008)

Registry entries: Bio.tools SciCrunch Bioconda

diamond-aligner

??? missing short description for package diamond-aligner :-(

https://github.com/bbuchfink/diamond

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package diamond-aligner
Release	Version	Architectures
bullseye	2.0.7-1	amd64,arm64
trixie	2.1.11-2	amd64,arm64,ppc64el,riscv64,s390x
bookworm	2.1.3-1	amd64,arm64,ppc64el,s390x
sid	2.1.14-1	amd64,arm64,loong64,ppc64el,riscv64,s390x
forky	2.1.14-1	amd64,arm64,loong64,ppc64el,riscv64,s390x
upstream	2.2.0

Popcon: 4 users (36 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Benjamin Buchfink, Chao Xie and Daniel H Huson: Fast and sensitive protein alignment using DIAMOND. (PubMed) Nature methods 12(1):59-60 (2015)

Registry entries: Bio.tools SciCrunch Bioconda

discosnp

??? missing short description for package discosnp :-(

http://colibread.inria.fr/discosnp/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package discosnp
Release	Version	Architectures
bullseye	4.4.4-1	amd64,arm64,i386
forky	2.6.2-5	amd64,arm64,ppc64el,riscv64
sid	2.6.2-5	amd64,arm64,loong64,ppc64el,riscv64
trixie	2.6.2-4	amd64,arm64,ppc64el,riscv64
bookworm	2.6.2-2	amd64,arm64,mips64el,ppc64el

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License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools SciCrunch Bioconda

disulfinder

??? missing short description for package disulfinder :-(

https://disulfind.dsi.unifi.it/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package disulfinder
Release	Version	Architectures
bookworm	1.2.11-12	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.2.11-13	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.2.11-13	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.2.11-12	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	1.2.11-10	amd64,arm64,armhf,i386

Popcon: 7 users (33 upd.)^*

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Please cite: Alessio Ceroni, Andrea Passerini, Alessandro Vullo and Paolo Frasconi: DISULFIND: a disulfide bonding state and cysteine connectivity prediction server. (PubMed) Nucleic Acids Res 34(Web Server issue):W177-181 (2006)

Registry entries: Bio.tools SciCrunch

dnaclust

??? missing short description for package dnaclust :-(

https://dnaclust.sourceforge.net/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package dnaclust
Release	Version	Architectures
sid	3-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	3-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	3-7	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	3-7	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	3-7	amd64,arm64,armhf,i386

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License: DFSG free

Official Debian package

Git

Please cite: Mohammadreza Ghodsi, Bo Liu and Mihai Pop: DNACLUST: accurate and efficient clustering of phylogenetic marker genes. (PubMed,eprint) BMC Bioinformatics 12:271 (2011)

Registry entries: Bio.tools SciCrunch

dnarrange

??? missing short description for package dnarrange :-(

https://github.com/mcfrith/dnarrange

Maintainer: Debian Med Packaging Team (Andreas Tille)

Popcon: 6 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

dotter

??? missing short description for package dotter :-(

https://www.sanger.ac.uk/science/tools/seqtools

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package dotter
Release	Version	Architectures
trixie	4.44.1+dfsg-7.1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	4.44.1+dfsg-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	4.44.1+dfsg-6	amd64,arm64,armhf,i386
bookworm	4.44.1+dfsg-7	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 5 users (36 upd.)^*

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License: DFSG free

Official Debian package

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Please cite: Gemma Barson and Ed Griffiths: SeqTools: visual tools for manual analysis of sequence alignments. (PubMed,eprint) BMC Research Notes 9:39 (2016)

Registry entries: Bio.tools SciCrunch

drop-seq-tools

??? missing short description for package drop-seq-tools :-(

https://github.com/broadinstitute/Drop-seq/

Maintainer: Debian Med Packaging Team (Pierre Gruet)

Versions of package drop-seq-tools
Release	Version	Architectures
bullseye	2.4.0+dfsg-6	all
bookworm	2.5.2+dfsg-1	all
trixie	3.0.2+dfsg-1	all
forky	3.0.2+dfsg-2	all
sid	3.0.2+dfsg-2	all

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Git

Registry entries: Bioconda

dssp

??? missing short description for package dssp :-(

https://github.com/PDB-REDO/dssp

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package dssp
Release	Version	Architectures
trixie	4.4.10-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	4.6.1-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	4.5.7-1	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
bullseye	4.0.0-2	amd64,arm64,armhf,i386
bookworm	4.2.2-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

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Please cite: W. Kabsch and C. Sander: Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.. (PubMed) Biopolymers 22:2577-2637 (1983)

Registry entries: Bio.tools SciCrunch

dwgsim

??? missing short description for package dwgsim :-(

https://github.com/nh13/DWGSIM/

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package dwgsim
Release	Version	Architectures
bullseye	0.1.12-4	amd64,arm64,armhf,i386
forky	0.1.14-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	0.1.14-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	0.1.14-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	0.1.14-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
upstream	0.1.16

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Newer upstream!

License: DFSG free

Official Debian package

Git

Registry entries: SciCrunch Bioconda

e-mem

??? missing short description for package e-mem :-(

https://www.csd.uwo.ca/~ilie/E-MEM/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package e-mem
Release	Version	Architectures
bullseye	1.0.1-4	amd64,arm64,armhf,i386
bookworm	1.0.1-5	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.0.1-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	1.0.1-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.0.1-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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Please cite: Nilesh Khiste and Lucian Ilie: E-MEM: efficient computation of maximal exact matches for very large genomes. (PubMed,eprint) Bioinformatics 31(4):509-514 (2015)

ea-utils

??? missing short description for package ea-utils :-(

https://expressionanalysis.github.io/ea-utils/

Maintainer: Debian Med Packaging Team (Charles Plessy)

Versions of package ea-utils
Release	Version	Architectures
trixie	1.1.2+dfsg-9	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	1.1.2+dfsg-6	amd64,arm64,armhf,i386
sid	1.1.2+dfsg-10	amd64,arm64,loong64,ppc64el,riscv64
bookworm	1.1.2+dfsg-9	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

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Please cite: Erik Aronesty: Comparison of Sequencing Utility Programs. (eprint) The Open Bioinformatics Journal 7:1-8 (2013)

Registry entries: Bio.tools SciCrunch

ecopcr

??? missing short description for package ecopcr :-(

https://git.metabarcoding.org/obitools/ecopcr/wikis/home

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package ecopcr
Release	Version	Architectures
trixie	1.0.1+dfsg-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	1.0.1+dfsg-2	amd64,arm64,armhf,i386
forky	1.0.1+dfsg-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.0.1+dfsg-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.0.1+dfsg-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

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Registry entries: Bioconda

edtsurf

??? missing short description for package edtsurf :-(

https://zhanglab.ccmb.med.umich.edu/EDTSurf/

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package edtsurf
Release	Version	Architectures
trixie	0.2009-10	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	0.2009-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	0.2009-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	0.2009-10	amd64,arm64,armhf,i386
bookworm	0.2009-10	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

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Please cite: Dong Xu and Yang Zhang: Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform.. (PubMed,eprint) PLoS ONE 4(12):e8140 (2009)

eigensoft

??? missing short description for package eigensoft :-(

http://www.hsph.harvard.edu/faculty/alkes-price/software/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package eigensoft
Release	Version	Architectures
forky	8.0.0+dfsg-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	8.0.0+dfsg-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	8.0.0+dfsg-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	8.0.0+dfsg-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	7.2.1+dfsg-2	amd64,arm64,armhf,i386

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Please cite: Alkes L. Price, Nick J. Patterson, Robert M. Plenge, Michael E. Weinblatt, Nancy A. Shadick and David Reich: Principal components analysis corrects for stratification in genome-wide association studies. Nature Genetics 38:904 - 909 (2006)

Registry entries: Bio.tools SciCrunch Bioconda

elph

??? missing short description for package elph :-(

https://www.cbcb.umd.edu/software/ELPH/

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package elph
Release	Version	Architectures
forky	1.0.1-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.0.1-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.0.1-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.0.1-5	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.0.1-5	amd64,arm64,armhf,i386

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embassy-domainatrix

??? missing short description for package embassy-domainatrix :-(

https://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMAINATRIX

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package embassy-domainatrix
Release	Version	Architectures
forky	0.1.660-5	amd64,arm64,loong64,ppc64el,riscv64
bullseye	0.1.660-4	amd64,arm64,armhf,i386
trixie	0.1.660-5	amd64,arm64,ppc64el,riscv64
bookworm	0.1.660-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	0.1.660-5	amd64,arm64,loong64,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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embassy-domalign

??? missing short description for package embassy-domalign :-(

https://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMALIGN

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package embassy-domalign
Release	Version	Architectures
trixie	0.1.660-5	amd64,arm64,ppc64el,riscv64
bookworm	0.1.660-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	0.1.660-4	amd64,arm64,armhf,i386
forky	0.1.660-5	amd64,arm64,loong64,ppc64el,riscv64
sid	0.1.660-5	amd64,arm64,loong64,ppc64el,riscv64

Debtags of package embassy-domalign:
field	biology, biology:bioinformatics
interface	commandline
role	program
scope	utility
use	analysing, comparing, editing
works-with-format	plaintext

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embassy-domsearch

??? missing short description for package embassy-domsearch :-(

https://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMSEARCH

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package embassy-domsearch
Release	Version	Architectures
forky	0.1.660-4	amd64,arm64,loong64,ppc64el,riscv64
bullseye	0.1.660-3	amd64,arm64,armhf,i386
bookworm	0.1.660-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	0.1.660-4	amd64,arm64,loong64,ppc64el,riscv64
trixie	0.1.660-4	amd64,arm64,ppc64el,riscv64

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emboss

??? missing short description for package emboss :-(

https://emboss.sourceforge.net

Maintainer: Debian Med Packaging Team (Andrius Merkys)

Versions of package emboss
Release	Version	Architectures
sid	6.6.0+dfsg-18	amd64,arm64,loong64,ppc64el,riscv64,s390x
bookworm	6.6.0+dfsg-12	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	6.6.0+dfsg-15	amd64,arm64,ppc64el,riscv64
forky	6.6.0+dfsg-18	amd64,arm64,loong64,ppc64el,riscv64,s390x
bullseye	6.6.0+dfsg-9	amd64,arm64,armhf,i386

Debtags of package emboss:
field	biology, biology:bioinformatics, biology:molecular
interface	commandline
role	program
scope	suite
use	analysing, comparing, converting, editing, organizing, searching, text-formatting, typesetting, viewing
works-with	db
works-with-format	plaintext

Popcon: 25 users (37 upd.)^*

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The package is enhanced by the following packages: clustalw primer3

Please cite: Peter Rice, Ian Longden and Alan Bleasby: EMBOSS: The European Molecular Biology Open Software Suite. (PubMed) Trends in Genetics 16(6):276 - 277 (2000)

Registry entries: Bio.tools SciCrunch Bioconda

emmax

??? missing short description for package emmax :-(

http://genome.sph.umich.edu/wiki/EMMAX

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package emmax
Release	Version	Architectures
forky	0~beta.20100307-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	0~beta.20100307-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	0~beta.20100307-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	0~beta.20100307-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	0~beta.20100307-1	amd64,arm64,armhf,i386

Popcon: 4 users (33 upd.)^*

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License: DFSG free

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Please cite: Hyun Min Kang, Jae Hoon Sul, Susan K Service, Noah A Zaitlen, Sit-yee Kong, Nelson B Freimer, Chiara Sabatti and Eleazar Eskin: Variance component model to account for sample structure in genome-wide association studies. (PubMed) Nature Genetics 42(4):348-54 (2010)

Registry entries: Bio.tools

estscan

??? missing short description for package estscan :-(

http://estscan.sourceforge.net/

Maintainer: Debian Med Packaging Team (Shruti Sridhar)

Versions of package estscan
Release	Version	Architectures
sid	3.0.3-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	3.0.3-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	3.0.3-6	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	3.0.3-5	amd64,arm64,armhf,i386
trixie	3.0.3-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 6 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: C. Lottaz, C. Iseli, CV. Jongeneel and Philipp Bucher: Modeling sequencing errors by combining Hidden Markov models Bioinformatics 19:103-112 (2003)

Registry entries: Bio.tools SciCrunch Bioconda

Remark of Debian Med team: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

examl

??? missing short description for package examl :-(

https://github.com/stamatak/ExaML

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package examl
Release	Version	Architectures
bookworm	3.0.22-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	3.0.22-1	amd64,arm64,armhf,i386
trixie	3.0.22-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	3.0.22-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	3.0.22-7	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x

Popcon: 5 users (38 upd.)^*

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License: DFSG free

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Git

Please cite: Alexey M. Kozlov, Andre J. Aberer and Alexandros Stamatakis: ExaML version 3: a tool for phylogenomic analyses on supercomputers. (PubMed,eprint) Bioinformatics 31(15):2577-2579 (2015)

exonerate

??? missing short description for package exonerate :-(

https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package exonerate
Release	Version	Architectures
forky	2.4.0-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	2.4.0-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2.4.0-5	amd64,arm64,armhf,i386
bookworm	2.4.0-5	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	2.4.0-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Debtags of package exonerate:
field	biology, biology:bioinformatics
interface	commandline
role	program
scope	utility
use	searching
works-with-format	plaintext

Popcon: 134 users (23 upd.)^*

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License: DFSG free

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Please cite: Guy C. Slater and Ewan Birney: Automated generation of heuristics for biological sequence comparison. (PubMed,eprint) BMC Bioinformatics 6(1):31 (2005)

Registry entries: Bio.tools SciCrunch Bioconda

fasta3

??? missing short description for package fasta3 :-(

https://fasta.bioch.virginia.edu

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package fasta3
Release	Version	Architectures
sid	36.3.8i.14-Nov-2020-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	36.3.8i.14-Nov-2020-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	36.3.8i.14-Nov-2020-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	36.3.8i.14-Nov-2020-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	36.3.8h.2020-02-11-3	amd64,arm64,armhf,i386

Popcon: 11 users (32 upd.)^*

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Please cite: William R. Pearson and D. J. Lipman: Improved tools for biological sequence comparison. (PubMed,eprint) Proc Natl Acad Sci U S A 85(8):2444-8 (1988)

Registry entries: Bioconda

fastahack

??? missing short description for package fastahack :-(

https://github.com/ekg/fastahack

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package fastahack
Release	Version	Architectures
sid	1.0.0+dfsg-11	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.0.0+dfsg-7	amd64,arm64,armhf,i386
bookworm	1.0.0+dfsg-10	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.0.0+dfsg-11	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.0.0+dfsg-11	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 5 users (34 upd.)^*

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Registry entries: Bioconda

fastani

??? missing short description for package fastani :-(

https://github.com/ParBLiSS/FastANI

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package fastani
Release	Version	Architectures
trixie	1.33-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.33-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	1.34+ds-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.34+ds-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 4 users (34 upd.)^*

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License: DFSG free

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fastaq

??? missing short description for package fastaq :-(

https://github.com/sanger-pathogens/Fastaq

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package fastaq
Release	Version	Architectures
bullseye	3.17.0-3	all
bookworm	3.17.0-5	all
trixie	3.17.0-9	all
sid	3.17.0-9	all
forky	3.17.0-9	all

Popcon: 9 users (33 upd.)^*

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License: DFSG free

Official Debian package

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Topics: Bioinformatics

fastdnaml

??? missing short description for package fastdnaml :-(

https://www.life.illinois.edu/gary/programs/fastDNAml.html

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package fastdnaml
Release	Version	Architectures
trixie	1.2.2-18	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	1.2.2-15	amd64,arm64,armhf,i386
sid	1.2.2-18	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.2.2-18	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.2.2-15	amd64,arm64,armel,armhf,i386,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

Popcon: 8 users (34 upd.)^*

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Please cite: Gary J. Olsen, Hideo Matsuda, Ray Hagstrom and Ross Overbeek: fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. (PubMed,eprint) Comput Appl Biosci 10(1):41-48 (1994)

fastlink

??? missing short description for package fastlink :-(

https://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package fastlink
Release	Version	Architectures
sid	4.1P-fix100+dfsg-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	4.1P-fix100+dfsg-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	4.1P-fix100+dfsg-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	4.1P-fix100+dfsg-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	4.1P-fix100+dfsg-4	amd64,arm64,armhf,i386

Popcon: 5 users (35 upd.)^*

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Please cite: R. W. Cottingham Jr., R. M. Idury and A. A. Schaffer: Faster Sequential Genetic Linkage Computations. (PubMed,eprint) American Journal of Human Genetics 53(1):252-263 (1993)

Registry entries: SciCrunch

fastml

??? missing short description for package fastml :-(

http://fastml.tau.ac.il/

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package fastml
Release	Version	Architectures
trixie	3.11-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	3.11-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	3.11-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	3.11-3	amd64,arm64,armhf,i386
sid	3.11-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 7 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Haim Ashkenazy, Osnat Penn, Adi Doron-Faigenboim, Ofir Cohen, Gina Cannarozzi, Oren Zomer and Tal Pupko: FastML: a web server for probabilistic reconstruction of ancestral sequences. (PubMed,eprint) Nucleic Acids Research 40(Web Server issue):W580-W584 (2012)

Registry entries: Bio.tools

fastp

??? missing short description for package fastp :-(

https://github.com/OpenGene/fastp

Maintainer: Debian Med Packaging Team (Dylan Aïssi)

Versions of package fastp
Release	Version	Architectures
bullseye	0.20.1+dfsg-1	amd64,arm64,armhf,i386
sid	1.0.1+dfsg-1	amd64,arm64,loong64,ppc64el,riscv64,s390x
forky	1.0.1+dfsg-1	amd64,arm64,loong64,ppc64el,riscv64,s390x
bookworm	0.23.2+dfsg-2	amd64,arm64,armel,armhf,mips64el,mipsel,ppc64el,s390x
trixie	0.24.0+dfsg-1	amd64,arm64,ppc64el,riscv64,s390x
upstream	1.3.3

Popcon: 7 users (35 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: multiqc

Please cite: Shifu Chen, Yanqing Zhou, Yaru Chen and Jia Gu: fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34(17):i884-i890 (2018)

Registry entries: Bioconda

fastq-pair

??? missing short description for package fastq-pair :-(

https://github.com/linsalrob/fastq-pair

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package fastq-pair
Release	Version	Architectures
bookworm	1.0-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.0-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.0-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.0-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 4 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

fastqc

??? missing short description for package fastqc :-(

https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Maintainer: Debian Med Packaging Team (Pierre Gruet)

Versions of package fastqc
Release	Version	Architectures
trixie	0.12.1+dfsg-4	all
bookworm	0.11.9+dfsg-6	all
forky	0.12.1+dfsg-4	all
bullseye	0.11.9+dfsg-4	all
sid	0.12.1+dfsg-4	all

Popcon: 26 users (36 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: multiqc

Registry entries: Bio.tools SciCrunch Bioconda

Topics: Sequencing

fastqtl

??? missing short description for package fastqtl :-(

http://fastqtl.sourceforge.net/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package fastqtl
Release	Version	Architectures
bullseye	2.184+dfsg-7	amd64,arm64,armhf,i386
sid	2.184+v7+dfsg-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	2.184+v7+dfsg-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	2.184+v7+dfsg-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	2.184+v7+dfsg-5	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x

Popcon: 8 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: fastqtl-doc

Please cite: Halit Ongen, Alfonso Buil, Andrew Anand Brown, Emmanouil T. Dermitzakis and and Olivier Delaneau: Fast and efficient QTL mapper for thousands of molecular phenotypes. (eprint) Bioinformatics (2015)

fasttree

??? missing short description for package fasttree :-(

http://www.microbesonline.org/fasttree/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package fasttree
Release	Version	Architectures
forky	2.1.11-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2.1.11-2	amd64,arm64,armhf,i386
sid	2.1.11-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	2.1.11-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	2.1.11-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 8 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Morgan N. Price, Paramvir S. Dehal and Adam P. Arkin: FastTree 2 -- Approximately Maximum-Likelihood Trees for Large Alignments.. (PubMed,eprint) PLoS ONE 5(3):e9490 (2010)

Registry entries: Bio.tools SciCrunch Bioconda

ffindex

??? missing short description for package ffindex :-(

https://github.com/ahcm/ffindex

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package ffindex
Release	Version	Architectures
bullseye	0.9.9.9-4	amd64,arm64,armhf,i386
bookworm	0.9.9.9-6	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	0.9.9.9-7	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	0.9.9.9-7	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
sid	0.9.9.9-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 4 users (1 upd.)^*

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License: DFSG free

Official Debian package

Git

figtree

??? missing short description for package figtree :-(

http://tree.bio.ed.ac.uk/software/figtree/

Maintainer: Debian Med Packaging Team (Pierre Gruet)

Popcon: 9 users (42 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools SciCrunch Bioconda

filtlong

??? missing short description for package filtlong :-(

https://github.com/rrwick/Filtlong

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package filtlong
Release	Version	Architectures
bookworm	0.2.1-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	0.3.1-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	0.2.0-2	amd64,arm64,armhf,i386
trixie	0.2.1-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	0.3.1-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 3 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools Bioconda

fitgcp

??? missing short description for package fitgcp :-(

http://sourceforge.net/projects/fitgcp/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package fitgcp
Release	Version	Architectures
trixie	0.0.20150429-5	all
forky	0.0.20150429-5	all
sid	0.0.20150429-5	all
bookworm	0.0.20150429-5	all
bullseye	0.0.20150429-4	all

Popcon: 5 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Martin S. Lindner, Maximilian Kollock, Franziska Zickmann and Bernhard Y. Renard: Analyzing genome coverage profiles with applications to quality control in metagenomics. (PubMed,eprint) Bioinformatics 29(10):1260-1267 (2013)

Registry entries: SciCrunch

flash

??? missing short description for package flash :-(

https://ccb.jhu.edu/software/FLASH/

Maintainer: Debian Med Packaging Team (Pranav Ballaney)

Versions of package flash
Release	Version	Architectures
bookworm	1.2.11-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.2.11-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.2.11-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.2.11-2	amd64,arm64,armhf,i386
sid	1.2.11-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 5 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: multiqc

Please cite: Tanja Magoč and Steven L Salzberg: FLASH: Fast Length Adjustment of Short Reads to Improve Genome Assemblies. (PubMed,eprint) Bioinformatics 27(21):2957-2963 (2011)

Registry entries: Bio.tools Bioconda

flexbar

??? missing short description for package flexbar :-(

https://github.com/seqan/flexbar

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package flexbar
Release	Version	Architectures
sid	3.5.0-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	3.5.0-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	3.5.0-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	3.5.0-5	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	3.5.0-3	amd64,arm64,armhf,i386

Popcon: 7 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: multiqc

Please cite: Matthias Dodt, Johannes T. Roehr, Rina Ahmed and Christoph Dieterich: FLEXBAR — Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms. (eprint) Biology 1(3):895-905 (2012)

Registry entries: Bio.tools SciCrunch Bioconda

flye

??? missing short description for package flye :-(

https://github.com/fenderglass/Flye

Maintainer: Debian Med Packaging Team (Alexandre Detiste)

Versions of package flye
Release	Version	Architectures
trixie	2.9.5+dfsg-1	amd64,arm64,ppc64el,riscv64,s390x
forky	2.9.6+dfsg-2	amd64,arm64,loong64,ppc64el,riscv64,s390x
sid	2.9.6+dfsg-2	amd64,arm64,loong64,ppc64el,riscv64,s390x
bookworm	2.9.1+dfsg-1	amd64,arm64,mips64el,ppc64el,s390x

Popcon: 5 users (35 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin and Pavel A. Pevzner: Assembly of long, error-prone reads using repeat graphs. (PubMed) Nature Biotechnology 37(5):540–546 (2019)

Registry entries: Bio.tools Bioconda

fml-asm

??? missing short description for package fml-asm :-(

https://github.com/lh3/fermi-lite

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package fml-asm
Release	Version	Architectures
bullseye	0.1+git20190320.b499514-1	amd64,arm64,armhf,i386
trixie	0.1+git20221215.85f159e-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	0.1+git20221215.85f159e-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	0.1+git20221215.85f159e-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	0.1+git20190320.b499514-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 3 users (38 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools SciCrunch Bioconda

freebayes

??? missing short description for package freebayes :-(

https://github.com/ekg/freebayes

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package freebayes
Release	Version	Architectures
bullseye	1.3.5-1	amd64,arm64,armhf,i386
bookworm	1.3.6-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.3.9-1	amd64,arm64,ppc64el,riscv64
experimental	1.3.7-1~exp	amd64,arm64,armhf,i386,ppc64el,s390x
sid	1.3.9-2	amd64,arm64,loong64,ppc64el,riscv64
upstream	1.3.10

Popcon: 7 users (32 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: Erik Garrison and Gabor Marth: Haplotype-based variant detection from short-read sequencing. (eprint) arXiv (2012)

Registry entries: Bio.tools SciCrunch Bioconda

freecontact

??? missing short description for package freecontact :-(

https://rostlab.org/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package freecontact
Release	Version	Architectures
bookworm	1.0.21-13	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	1.0.21-16	amd64,arm64,loong64,ppc64el,riscv64,s390x
trixie	1.0.21-15	amd64,arm64,ppc64el,riscv64,s390x
bullseye	1.0.21-9	amd64,arm64,armhf,i386
sid	1.0.21-16	amd64,arm64,loong64,ppc64el,riscv64,s390x

Popcon: 7 users (35 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: László Kaján, Thomas A. Hopf, Matúš Kalaš, Debora S. Marks and Burkhard Rost: FreeContact: fast and free software for protein contact prediction from residue co-evolution. BMC Bioinformatics (2014)

Topics: Structure prediction; Sequence analysis

fsa

??? missing short description for package fsa :-(

http://fsa.sourceforge.net/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package fsa
Release	Version	Architectures
forky	1.15.9+dfsg-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.15.9+dfsg-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.15.9+dfsg-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.15.9+dfsg-6	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.15.9+dfsg-6	amd64,arm64,armhf,i386

Popcon: 130 users (20 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Robert K. Bradley, Adam Roberts, Michael Smoot, Sudeep Juvekar, Jaeyoung Do, Colin Dewey, Ian Holmes and Lior Pachter: Fast Statistical Alignment. (PubMed,eprint) PLoS Comput Biol. 5(5):e1000392 (2009)

Registry entries: Bioconda

Remark of Debian Med team: Precondition for T-Coffee

see http://wiki.debian.org/DebianMed/TCoffee

Upstream address bounced when contacting about segfaults so it seems to be dead upstream and no good code quality.

fsm-lite

??? missing short description for package fsm-lite :-(

https://github.com/nvalimak/fsm-lite

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package fsm-lite
Release	Version	Architectures
forky	1.0-8	amd64,arm64,loong64,ppc64el,riscv64,s390x
bullseye	1.0-5	amd64,arm64
bookworm	1.0-8	amd64,arm64,mips64el,ppc64el,s390x
trixie	1.0-8	amd64,arm64,ppc64el,riscv64,s390x
sid	1.0-8	amd64,arm64,loong64,ppc64el,riscv64,s390x

Popcon: 4 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Registry entries: SciCrunch Bioconda

gamgi

??? missing short description for package gamgi :-(

http://www.gamgi.org/

Maintainer: Debichem Team (Andreas Tille)

Versions of package gamgi
Release	Version	Architectures
bullseye	0.17.3-3	amd64,arm64,armhf,i386
bookworm	0.17.5-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 7 users (0 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: gamgi-data gamgi-doc

Registry entries: SciCrunch

garli

??? missing short description for package garli :-(

https://github.com/Ashod/garli

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package garli
Release	Version	Architectures
forky	2.1-9	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
trixie	2.1-9	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	2.1-9	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2.1-4	amd64,arm64,armhf,i386
bookworm	2.1-7	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 5 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

garlic

??? missing short description for package garlic :-(

http://www.zucic.org/garlic/

Maintainer: Debichem Team (Andreas Tille)

Versions of package garlic
Release	Version	Architectures
sid	1.6-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.6-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.6-3	amd64,arm64,armhf,i386
bookworm	1.6-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.6-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 20 users (38 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Damir Zucic and Davor Juretic: Precise Annotation of Transmembrane Segments with Garlic - a Free Molecular Visualization Program (eprint) Croatica Chemica Acta 77(1-2):397-401 (2004)

Registry entries: Bio.tools

gasic

??? missing short description for package gasic :-(

http://sourceforge.net/projects/gasic/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package gasic
Release	Version	Architectures
forky	0.0.r19-8	all
bookworm	0.0.r19-8	all
bullseye	0.0.r19-7	all
sid	0.0.r19-8	all
trixie	0.0.r19-8	all

Popcon: 5 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: gasic-examples

Please cite: Martin S. Lindner and Bernhard Y. Renard: Metagenomic abundance estimation and diagnostic testing on species level. (PubMed,eprint) Nucleic Acids Research 41(1):e10 (2013)

Registry entries: SciCrunch

gatb-core

??? missing short description for package gatb-core :-(

https://github.com/GATB/gatb-core

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package gatb-core
Release	Version	Architectures
forky	1.4.2+dfsg-13	amd64,arm64,ppc64el,riscv64
sid	1.4.2+dfsg-13	amd64,arm64,loong64,ppc64el,riscv64
bullseye	1.4.2+dfsg-6	amd64,arm64,i386
bookworm	1.4.2+dfsg-11	amd64,arm64,mips64el,ppc64el
trixie	1.4.2+dfsg-13	amd64,arm64,ppc64el,riscv64

Popcon: 7 users (35 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Erwan Drezen, Guillaume Rizk, Rayan Chikhi, Charles Deltel, Claire Lemaitre, Pierre Peterlongo and Dominique Lavenier: GATB: Genome Assembly & Analysis Tool Box. Bioinformatics 30(20):2959-2961 (2014)

Registry entries: Bioconda

gdpc

??? missing short description for package gdpc :-(

https://web.archive.org/web/20180212152753/http://www.frantz.fi/software/gdpc.php

Maintainer: Debian Med Packaging Team (Yavor Doganov)

Versions of package gdpc
Release	Version	Architectures
bullseye	2.2.5-14	amd64,arm64
bookworm	2.2.5-15	amd64,arm64,mips64el,ppc64el
trixie	2.2.5-16	amd64,arm64,ppc64el,riscv64
forky	2.2.5-19	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
sid	2.2.5-19	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Debtags of package gdpc:
field	biology, biology:structural, chemistry, physics
interface	x11
role	program
scope	application
uitoolkit	gtk
use	viewing
works-with	3dmodel, image, video
works-with-format	jpg, png
x11	application

Popcon: 14 users (45 upd.)^*

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License: DFSG free

Official Debian package

Git

gemma

??? missing short description for package gemma :-(

https://www.xzlab.org/software.html

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package gemma
Release	Version	Architectures
trixie	0.98.5+dfsg-3	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
sid	0.98.5+dfsg-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	0.98.4+dfsg-4	amd64,arm64,armhf,i386
bookworm	0.98.5+dfsg-2	amd64,arm64,armhf,i386,mips64el,ppc64el,s390x

Popcon: 5 users (32 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Xiang Zhou and Matthew Stephens: Genome-wide efficient mixed-model analysis for association studies Nature Genetics 44:821-824 (2012)

Registry entries: Bioconda

genometester

??? missing short description for package genometester :-(

https://github.com/bioinfo-ut/GenomeTester4

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package genometester
Release	Version	Architectures
bookworm	4.0+git20200511.91cecb5+dfsg-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	4.0+git20221122.71e6625-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	4.0+git20200511.91cecb5+dfsg-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	4.0+git20221122.71e6625-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	4.0+git20200511.91cecb5+dfsg-1	amd64,arm64,armhf,i386

Popcon: 6 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Lauris Kaplinski, Maarja Lepamets and Maido Remm: GenomeTester4: a toolkit for performing basic set operations - union, intersection and complement on k-mer lists. (PubMed,eprint) GigaScience 4(1):58 (2015)

Registry entries: Bio.tools Bioconda

genomethreader

??? missing short description for package genomethreader :-(

https://genomethreader.org

Maintainer: Debian Med Packaging Team (Marcos Talau)

Versions of package genomethreader
Release	Version	Architectures
bookworm	1.7.3+dfsg-7	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	1.7.3+dfsg-12	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.7.3+dfsg-10	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	1.7.3+dfsg-12	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.7.3+dfsg-5	amd64,arm64,armhf,i386

Popcon: 8 users (37 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: G. Gremme, V. Brendel, M.E. Sparks and S. Kurtz: Engineering a software tool for gene structure prediction in higher organisms. Information and Software Technology 47(15):965-978 (2005)

Registry entries: Bio.tools Bioconda

genometools

??? missing short description for package genometools :-(

http://genometools.org

Maintainer: Debian Med Packaging Team (Sascha Steinbiss)

Versions of package genometools
Release	Version	Architectures
bookworm-backports	1.6.5+ds-2~bpo12+1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.6.5+ds-2.2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	1.6.1+ds-3	amd64,arm64,armhf,i386
sid	1.6.6+ds-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.6.6+ds-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.6.2+ds-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 6 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Gordon Gremme, Sascha Steinbiss and Stefan Kurtz: GenomeTools: a comprehensive software library for efficient processing of structured genome annotations.. (PubMed) IEEE/ACM Transactions on Computational Biology and Bioinformatics 10(3):645-656 (2013)

Registry entries: Bio.tools

genomicsdb-tools

??? missing short description for package genomicsdb-tools :-(

https://www.genomicsdb.org/

Maintainer: Debian Med Packaging Team (Pierre Gruet)

Versions of package genomicsdb-tools
Release	Version	Architectures
bookworm	1.4.4-3	amd64,mips64el
forky	1.5.5-2	amd64,arm64,armhf,ppc64el,riscv64,s390x
sid	1.5.5-2	amd64,arm64,armhf,loong64,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

gentle

??? missing short description for package gentle :-(

http://gentle.magnusmanske.de

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package gentle
Release	Version	Architectures
sid	1.9.5~alpha2+dfsg1-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.9+cvs20100605+dfsg1-10	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.9+cvs20100605+dfsg1-9	amd64,arm64,armhf,i386
forky	1.9.5~alpha2+dfsg1-3	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
trixie	1.9.5~alpha2+dfsg1-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

Please cite: Magnus Manske: GENtle, a free multi-purpose molecular biology tool. (eprint) (2006)

Registry entries: Bio.tools SciCrunch

gff2aplot

??? missing short description for package gff2aplot :-(

https://genome.crg.es/software/gfftools/GFF2APLOT.html

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package gff2aplot
Release	Version	Architectures
bullseye	2.0-13	amd64,arm64,armhf,i386
sid	2.0-15	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	2.0-15	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	2.0-15	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	2.0-14	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,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

Popcon: 6 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: J. F. Abril, R. Guigó and T. Wiehe: gff2aplot: Plotting sequence comparisons. (PubMed,eprint) Bioinformatics 19(18):2477-2479 (2003)

Registry entries: Bio.tools

gff2ps

??? missing short description for package gff2ps :-(

https://genome.crg.es/software/gff2ps/

Maintainer: Debian Med Packaging Team (Andreas Tille)

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

Popcon: 6 users (32 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: J. F. Abril and R. Guigó: gff2ps: visualizing genomic annotations.. (PubMed,eprint) Bioinformatics 16(8):743-744 (2000)

Registry entries: Bio.tools SciCrunch

gffread

??? missing short description for package gffread :-(

https://ccb.jhu.edu/software/stringtie/gff.shtml

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package gffread
Release	Version	Architectures
bullseye	0.12.1-4	amd64,arm64,armhf,i386
bookworm	0.12.7-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	0.12.7-8	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	0.12.7-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	0.12.7-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
upstream	0.12.9

Popcon: 5 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools Bioconda

ggd-utils

??? missing short description for package ggd-utils :-(

https://github.com/gogetdata/ggd-utils

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package ggd-utils
Release	Version	Architectures
bullseye	0.0.7+ds-3	amd64,arm64,armhf,i386
sid	1.0.0+ds-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.0.0+ds-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.0.0+ds-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.0.0+ds-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

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License: DFSG free

Official Debian package

Git

ghmm

??? missing short description for package ghmm :-(

https://sourceforge.net/p/ghmm/wiki/Home/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package ghmm
Release	Version	Architectures
sid	0.9~rc3-12	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	0.9~rc3-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	0.9~rc3-4	amd64,arm64,armhf,i386
trixie	0.9~rc3-11	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	0.9~rc3-12	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 6 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

glam2

??? missing short description for package glam2 :-(

https://meme-suite.org/meme/doc/glam2.html?man_type=web

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package glam2
Release	Version	Architectures
bullseye	1064-9	amd64,arm64,armhf,i386
forky	1064-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1064-9	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1064-10	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	1064-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Debtags of package glam2:
field	biology, biology:bioinformatics
interface	commandline
role	program
scope	utility
use	analysing, comparing, searching
works-with-format	plaintext

Popcon: 8 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Martin C. Frith, Neil F. W. Saunders, Bostjan Kobe and Timothy L. Bailey: Discovering Sequence Motifs with Arbitrary Insertions and Deletions. (PubMed) PLoS Computational Biology 4(5):e1000071 (2008)

gmap

??? missing short description for package gmap :-(

http://research-pub.gene.com/gmap

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package gmap
Release	Version	Architectures
forky	2025-07-31+ds-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
sid	2025-07-31+ds-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
bookworm	2021-12-17+ds-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el
bullseye	2021-02-22+ds-1	amd64,arm64,armhf,i386
trixie	2024-11-20+ds-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64
upstream	2025-07-31.v2

Popcon: 8 users (34 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: Thomas D. Wu and Serban Nacu: Fast and SNP-tolerant detection of complex variants and splicing in short reads. (PubMed,eprint) Bioinformatics 26(7):873-81 (2010)

Registry entries: Bio.tools SciCrunch Bioconda

grabix

??? missing short description for package grabix :-(

https://github.com/arq5x/grabix

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package grabix
Release	Version	Architectures
bookworm	0.1.7-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	0.1.7-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	0.1.7-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	0.1.7-2	amd64,arm64,armhf,i386
sid	0.1.7-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 4 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

graphlan

??? missing short description for package graphlan :-(

https://huttenhower.sph.harvard.edu/graphlan

Maintainer: Debian Med Packaging Team (Alexandre Detiste)

Popcon: 6 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

grinder

??? missing short description for package grinder :-(

https://sourceforge.net/projects/biogrinder/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Popcon: 7 users (32 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Florent E. Angly, Dana Willner, Forest Rohwer, Philip Hugenholtz and Gene W. Tyson: Grinder: a versatile amplicon and shotgun sequence simulator. (PubMed,eprint) Nucleic Acids Research Epub ahead of print (2012)

Registry entries: SciCrunch

gromacs

??? missing short description for package gromacs :-(

https://www.gromacs.org/

Maintainer: Debichem Team (Santiago Vila)

Versions of package gromacs
Release	Version	Architectures
sid	2026.2-2	amd64,arm64,loong64,ppc64el,riscv64,s390x
bookworm	2022.5-2	amd64,arm64,mips64el,ppc64el,s390x
trixie	2025.2-1	amd64,arm64,ppc64el,riscv64,s390x
forky	2026.1-1	amd64,arm64,ppc64el,riscv64,s390x
bullseye	2020.6-2	amd64,arm64,armhf,i386

Popcon: 21 users (53 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Berk Hess, Carsten Kutzner, David van der Spoel and Erik Lindahl: GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. (eprint) J. Chem. Theory Comput. 4(3):435-447 (2008)

Registry entries: Bio.tools SciCrunch Bioconda

gsort

??? missing short description for package gsort :-(

https://github.com/brentp/gsort

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package gsort
Release	Version	Architectures
trixie	0.1.4-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	0.1.4-3	amd64,arm64,armhf,i386
bookworm	0.1.4-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	0.1.5-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	0.1.5-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 4 users (35 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

gubbins

??? missing short description for package gubbins :-(

https://nickjcroucher.github.io/gubbins/

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package gubbins
Release	Version	Architectures
trixie	3.4-2	amd64,i386
bookworm	2.4.1-5	amd64,i386
bullseye	2.4.1-4	amd64,i386
forky	3.4.3-4	amd64,i386
sid	3.4.3-4	amd64,i386

Popcon: 7 users (37 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Nicholas J. Croucher, Andrew J. Page, Thomas R. Connor, Aidan J. Delaney, Jacqueline A. Keane, Stephen D. Bentley, Julian Parkhill and Simon R. Harris: Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. (PubMed,eprint) Nucleic Acids Research 43(3):e15 (2014)

Registry entries: Bioconda

gwama

??? missing short description for package gwama :-(

https://genomics.ut.ee/en/tools

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package gwama
Release	Version	Architectures
trixie	2.2.2+dfsg-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	2.2.2+dfsg-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	2.2.2+dfsg-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2.2.2+dfsg-4	amd64,arm64,armhf,i386
bookworm	2.2.2+dfsg-5	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 4 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Reedik Mägi and Andrew P. Morris: GWAMA: software for genome-wide association meta-analysis. (eprint) BMC Bioinformatics 11(May):288 (2010)

Registry entries: Bio.tools SciCrunch Bioconda

harvest-tools

??? missing short description for package harvest-tools :-(

https://harvest.readthedocs.org/en/latest/content/harvest-tools.html

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package harvest-tools
Release	Version	Architectures
trixie	1.3-8	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.3-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.3-6	amd64,arm64,armhf,i386
bookworm	1.3-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.3-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 5 users (35 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Todd J. Treangen, Brian D. Ondov, Sergey Koren and Adam M. Phillippy: Rapid Core-Genome Alignment and Visualization for Thousands of Intraspecific Microbial Genomes. (PubMed,eprint) bioRxiv 15(11):524 (2014)

Registry entries: Bioconda

hhsuite

??? missing short description for package hhsuite :-(

https://toolkit.tuebingen.mpg.de/

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package hhsuite
Release	Version	Architectures
trixie	3.3.0+ds-8	amd64,arm64,armel,armhf,i386,ppc64el,riscv64
forky	3.3.0+ds-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
sid	3.3.0+ds-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
bullseye	3.3.0+ds-4	amd64,arm64,armhf,i386
bookworm	3.3.0+ds-7	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el

Popcon: 10 users (35 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Michael Remmert, Andreas Biegert, Andreas Hauser and Johannes Söding: HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment.. (PubMed) Nat. Methods 9(2):173-175 (2011)

Registry entries: SciCrunch Bioconda

hilive

??? missing short description for package hilive :-(

https://gitlab.com/rki_bioinformatics/HiLive2

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package hilive
Release	Version	Architectures
sid	2.0a-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2.0a-3	amd64,arm64,armhf,i386
bookworm	2.0a-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 0 users (0 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Martin S. Lindner, Benjamin Strauch, Jakob M. Schulze, Simon H. Tausch, Piotr W. Dabrowski, Andreas Nitsche and Bernhard Y. Renard: HiLive: real-time mapping of illumina reads while sequencing. (PubMed) Bioinformatics 33(6):917-919 (2017)

hisat2

??? missing short description for package hisat2 :-(

https://daehwankimlab.github.io/hisat2/

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package hisat2
Release	Version	Architectures
forky	2.2.1-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	2.2.1-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	2.2.1-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	2.2.1-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2.2.1-2	amd64,arm64,armhf,i386
upstream	2.2.2

Popcon: 11 users (41 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: multiqc

Please cite: Daehwan Kim, Joseph M. Paggi, Chanhee Park, Christopher Bennett and Steven L. Salzberg: Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature Biotechnology 37(8):907-915 (2019)

Registry entries: Bio.tools SciCrunch Bioconda

hmmer

??? missing short description for package hmmer :-(

http://hmmer.org/

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package hmmer
Release	Version	Architectures
bullseye	3.3.2+dfsg-1	amd64,i386
trixie	3.4+dfsg-2	amd64,arm64,i386
sid	3.4+dfsg-3	amd64,arm64,i386
bookworm	3.3.2+dfsg-1	amd64,i386
forky	3.4+dfsg-3	amd64,arm64,i386

Debtags of package hmmer:
biology	format:aln, peptidic
field	biology, biology:bioinformatics
interface	commandline
role	program
scope	utility
use	searching
works-with	db
works-with-format	plaintext

Popcon: 34 users (36 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: S. R. Eddy: Profile hidden Markov models. (PubMed,eprint) Bioinformatics 14(9):755-763 (1998)

Registry entries: Bio.tools SciCrunch Bioconda

hmmer2

??? missing short description for package hmmer2 :-(

https://hmmer.janelia.org/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package hmmer2
Release	Version	Architectures
bookworm	2.3.2+dfsg-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	2.3.2+dfsg-12	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	2.3.2+dfsg-12	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	2.3.2+dfsg-12	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2.3.2+dfsg-7	amd64,arm64,armhf,i386

Popcon: 6 users (35 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Eddy, Sean R.: Profile hidden Markov models. (PubMed) Bioinformatics 14(9):755-763 (1998)

Registry entries: Bio.tools SciCrunch Bioconda

Remark of Debian Med team: This older version of HMMER is used in some applications

While Debian has HMMER 3 since some time there are users of HMMER 2 interested in having this old version available and thus the package is reintroduced.

hyphy-mpi

??? missing short description for package hyphy-mpi :-(

https://hyphy.org/

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package hyphy-mpi
Release	Version	Architectures
bullseye	2.5.28+dfsg-3	amd64,arm64,armhf,i386
trixie	2.5.69+dfsg-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	2.5.69+dfsg-2	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
bookworm	2.5.47+dfsg-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	2.5.69+dfsg-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
upstream	2.5.98

Popcon: 6 users (34 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: Sergei L. Kosakovsky Pond, Simon D. W. Frost and Spencer V. Muse: HyPhy: hypothesis testing using phylogenies. (PubMed,eprint) Bioinformatics 21(5):676-679 (2005)

Registry entries: Bioconda

hyphy-pt

??? missing short description for package hyphy-pt :-(

https://hyphy.org/

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package hyphy-pt
Release	Version	Architectures
bullseye	2.5.28+dfsg-3	amd64,arm64,armhf,i386
bookworm	2.5.47+dfsg-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	2.5.69+dfsg-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	2.5.69+dfsg-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	2.5.69+dfsg-2	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
upstream	2.5.98

Popcon: 4 users (2 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Sergei L. Kosakovsky Pond, Simon D. W. Frost and Spencer V. Muse: HyPhy: hypothesis testing using phylogenies. (PubMed,eprint) Bioinformatics 21(5):676-679 (2005)

Registry entries: Bioconda

idba

??? missing short description for package idba :-(

https://github.com/loneknightpy/idba

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package idba
Release	Version	Architectures
sid	1.1.3-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.1.3-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.1.3-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.1.3-7	amd64,arm64,armhf,i386
trixie	1.1.3-8	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 8 users (32 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Yu Peng, Henry C. M. Leung, S. M. Yiu and Francis Y. L. Chin: IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. (PubMed,eprint) Bioinformatics 28(11):1420-1428 (2012)

Registry entries: Bio.tools SciCrunch Bioconda

igblast

??? missing short description for package igblast :-(

https://ncbi.github.io/igblast/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package igblast
Release	Version	Architectures
sid	1.20.0-4	amd64,arm64
bookworm	1.19.0-1	amd64,arm64,mips64el,ppc64el,s390x
forky	1.20.0-4	amd64,arm64
trixie	1.20.0-2	amd64,arm64
upstream	1.22.0

Popcon: 4 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Jian Ye, Ning Ma, Thomas L Madden and James M Ostell: IgBLAST: an immunoglobulin variable domain sequence analysis tool. (PubMed,eprint) Nucleic Acids Res. 41:W34-W40 (2013)

Registry entries: Bio.tools SciCrunch

igor

??? missing short description for package igor :-(

https://github.com/qmarcou/IGoR/

Maintainer: Debian Med Packaging Team (Lance Lin)

Versions of package igor
Release	Version	Architectures
forky	1.4.0+dfsg-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.4.0+dfsg-2	amd64,arm64,armhf,i386
bookworm	1.4.0+dfsg-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.4.0+dfsg-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	1.4.0+dfsg-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 5 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Quentin Marcou, Thierry Mora and Aleksandra M. Walczak: High-throughput immune repertoire analysis with IGoR. (PubMed,eprint) Nature Communications 9(1):561 (2018)

Registry entries: Bioconda

igv

??? missing short description for package igv :-(

https://www.broadinstitute.org/igv/

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package igv
Release	Version	Architectures
bookworm	2.16.0+dfsg-1	all
bullseye	2.6.3+dfsg-3 (non-free)	all
sid	2.18.5+dfsg-4	all
trixie	2.18.5+dfsg-1	all
upstream	2.19.7

Popcon: 7 users (31 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz and Jill P Mesirov: Integrative genomics viewer. (PubMed,eprint) Nature Biotechnology 29(1):24–26 (2011)

Registry entries: Bio.tools SciCrunch Bioconda

indelible

??? missing short description for package indelible :-(

http://abacus.gene.ucl.ac.uk/software/indelible/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package indelible
Release	Version	Architectures
trixie	1.03-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.03-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.03-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.03-5	amd64,arm64,armhf,i386
bookworm	1.03-5	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 5 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: William Fletcher and Ziheng Yang: INDELible: A Flexible Simulator of Biological Sequence Evolution. (eprint) Molecular Biology and Evolution 26(8):1879-1888 (2009)

Topics: Sequencing

infernal

??? missing short description for package infernal :-(

http://eddylab.org/infernal/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package infernal
Release	Version	Architectures
bullseye	1.1.4-1	amd64,i386
bookworm	1.1.4-1	amd64,i386
sid	1.1.5-3	amd64,arm64,i386
forky	1.1.5-3	amd64,arm64,i386
trixie	1.1.5-3	amd64,arm64,i386

Popcon: 14 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Eric P. Nawrocki, Diana L. Kolbe and Sean R. Eddy: Infernal 1.0: inference of RNA alignments. (PubMed,eprint) Bioinformatics 25(10):1335-1337 (2009)

Registry entries: SciCrunch Bioconda

insilicoseq

??? missing short description for package insilicoseq :-(

https://github.com/HadrienG/InSilicoSeq

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package insilicoseq
Release	Version	Architectures
sid	2.0.1-3	all
bookworm	1.5.4-6	all
trixie	2.0.1-1	all
bullseye	1.5.2-1	all
forky	2.0.1-2	all

Popcon: 6 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Hadrien Gourlé, Oskar Karlsson-Lindsjö, Juliette Hayer and Erik Bongcam-Rudloff: Simulating Illumina data with InSilicoSeq. Bioinformatics 35(3):521–522 (2019)

Registry entries: Bioconda

ipig

??? missing short description for package ipig :-(

http://sourceforge.net/projects/ipig/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package ipig
Release	Version	Architectures
bookworm	0.0.r5-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	0.0.r5-4	amd64,arm64,armhf,i386
forky	0.0.r5-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	0.0.r5-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	0.0.r5-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 4 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Mathias Kuhring and Bernhard Y. Renard: iPiG: Integrating Peptide Spectrum Matches into Genome Browser Visualizations. (PubMed,eprint) PLoS ONE 7(12):e50246 (2012)

Registry entries: Bio.tools SciCrunch

iqtree

??? missing short description for package iqtree :-(

http://www.iqtree.org/

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package iqtree
Release	Version	Architectures
bookworm	2.0.7+dfsg-1	amd64,i386
sid	2.4.0+dfsg-1	amd64
forky	2.4.0+dfsg-1	amd64
bullseye	1.6.12+dfsg-1	amd64,i386
trixie	2.0.7+dfsg-1	amd64,i386

Popcon: 7 users (36 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Lam Tung Nguyen, Heiko A. Schmidt, Arndt von Haeseler and Bui Quang Minh: IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. (PubMed,eprint) Mol. Biol. Evol. 32(1):268-274 (2015)

Registry entries: Bio.tools Bioconda

iva

??? missing short description for package iva :-(

https://github.com/sanger-pathogens/iva

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package iva
Release	Version	Architectures
forky	1.0.11+ds-6	amd64,arm64,armhf,i386,ppc64el,riscv64
bullseye	1.0.9+ds-11	amd64,arm64,armhf,i386
bookworm	1.0.11+ds-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el
trixie	1.0.11+ds-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64
sid	1.0.11+ds-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64

Popcon: 5 users (32 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: M. Hunt, A. Gall, S. H. Ong, J. Brener, B. Ferns, P. Goulder, E. Nastouli, J. A. Keane, P. Kellam and T. D. Otto: IVA: accurate de novo assembly of RNA virus genomes. (PubMed) Bioinformatics 31(14):2374-2376 (2015)

Registry entries: Bio.tools Bioconda

jaligner

??? missing short description for package jaligner :-(

https://github.com/ahmedmoustafa/JAligner

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package jaligner
Release	Version	Architectures
bookworm	1.0+dfsg-10	all
sid	1.0+dfsg-11	all
forky	1.0+dfsg-11	all
trixie	1.0+dfsg-11	all
bullseye	1.0+dfsg-7	all

Popcon: 4 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

jalview

??? missing short description for package jalview :-(

https://www.jalview.org

Maintainer: Debian Java Maintainers (Pierre Gruet)

Versions of package jalview
Release	Version	Architectures
sid	2.11.5.0+dfsg-2	all
trixie	2.11.4.1+dfsg-1	all
bookworm	2.11.2.5+dfsg-3	all
bullseye	2.11.1.3+dfsg2-5	all
upstream	2_11_5_1

Popcon: 6 users (34 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: Andrew M. Waterhouse, James B. Procter, David M. A. Martin, Michèle Clamp and Geoffrey J. Barton: Jalview Version 2-a multiple sequence alignment editor and analysis workbench. (PubMed,eprint) Bioinformatics 25:1189-1191 (2009)

Registry entries: Bio.tools SciCrunch Bioconda

jellyfish

??? missing short description for package jellyfish :-(

https://www.genome.umd.edu/jellyfish.html

Maintainer: Debian Med Packaging Team (Sergio Durigan Junior)

Versions of package jellyfish
Release	Version	Architectures
sid	2.3.1-6	amd64,arm64,loong64,ppc64el,riscv64
bullseye	2.3.0-10	amd64,arm64,armhf,i386
trixie	2.3.1-4	amd64,arm64,ppc64el,riscv64
bookworm	2.3.0-15	amd64,arm64,armel,armhf,i386,mips64el,ppc64el
forky	2.3.1-6	amd64,arm64,loong64,ppc64el,riscv64

Popcon: 8 users (39 upd.)^*

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: multiqc

Please cite: Guillaume Marcais and Carl Kingsford: A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27(6):764-770 (2011)

Registry entries: Bio.tools SciCrunch Bioconda

jellyfish1

??? missing short description for package jellyfish1 :-(

https://www.cbcb.umd.edu/software/jellyfish/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package jellyfish1
Release	Version	Architectures
sid	1.1.11-10	amd64,arm64,loong64,ppc64el,riscv64
bullseye	1.1.11-5	amd64,arm64,armhf,i386
bookworm	1.1.11-8	amd64,arm64,mips64el,ppc64el
trixie	1.1.11-10	amd64,arm64,ppc64el,riscv64
forky	1.1.11-10	amd64,arm64,loong64,ppc64el,riscv64

Popcon: 6 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Guillaume Marcais and Carl Kingsford: A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27(6):764-770 (2011)

Registry entries: Bio.tools SciCrunch

jmodeltest

??? missing short description for package jmodeltest :-(

https://github.com//ddarriba/jmodeltest2

Maintainer: Debian Med Packaging Team (Pierre Gruet)

Versions of package jmodeltest
Release	Version	Architectures
bookworm	2.1.10+dfsg-12	all
sid	2.1.10+dfsg-13	all
forky	2.1.10+dfsg-13	all
bullseye	2.1.10+dfsg-10	all

Popcon: 0 users (0 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Diego Darriba, Guillermo L Taboada, Ramón Doallo and David Posada: jModelTest 2: more models, new heuristics and parallel computing. (PubMed) Nature Methods 9(8):772 (2012)

Registry entries: SciCrunch

jmol

??? missing short description for package jmol :-(

https://jmol.sourceforge.net/

Maintainer: Debichem Team (Pierre Gruet)

Versions of package jmol
Release	Version	Architectures
bullseye	14.6.4+2016.11.05+dfsg1-4	all
trixie	16.2.33+dfsg-1	all
trixie-backports	16.3.55+dfsg-1~bpo13+1	all
forky	16.3.55+dfsg-1	all
sid	16.3.55+dfsg-1	all
bookworm	14.32.83+dfsg-2	all

Popcon: 42 users (54 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: A. Herráez: Biomolecules in the computer: Jmol to the rescue. (PubMed,eprint) Biochem Mol Biol Educ. 34(4):255-261 (2006)

Registry entries: SciCrunch

kalign

??? missing short description for package kalign :-(

https://msa.sbc.su.se/

Maintainer: Debian Med Packaging Team (Charles Plessy)

Versions of package kalign
Release	Version	Architectures
trixie	3.4.0-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	3.3.5-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	3.3-1	amd64,arm64,armhf,i386
sid	3.5.1-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	3.5.1-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Debtags of package kalign:
biology	format:aln, nuceleic-acids, peptidic
field	biology, biology:bioinformatics
interface	commandline
role	program
scope	utility
use	comparing
works-with-format	plaintext

Popcon: 17 users (50 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Lassmann, Timo.: Kalign 3: multiple sequence alignment of large datasets. (eprint) Bioinformatics 36(6):1928-1929 (2020)

Registry entries: Bio.tools SciCrunch

kallisto

??? missing short description for package kallisto :-(

https://pachterlab.github.io/kallisto

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package kallisto
Release	Version	Architectures
bullseye	0.46.2+dfsg-2	amd64,arm64,armhf,i386
trixie	0.48.0+dfsg-4	amd64,arm64,ppc64el,riscv64,s390x
sid	0.48.0+dfsg-4	ppc64el,riscv64
bookworm	0.48.0+dfsg-3	amd64,arm64,mips64el,ppc64el,s390x
sid	0.51.1+dfsg-1	amd64,arm64,loong64,s390x
upstream	0.52.0

Popcon: 4 users (33 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: multiqc

Please cite: Nicolas L Bray, Harold Pimentel, Páll Melsted and Lior Pachter: Near-optimal probabilistic RNA-seq quantification. (PubMed) Nature Biotechnology 34(5):525–527 (2016)

Registry entries: Bio.tools Bioconda

kaptive

??? missing short description for package kaptive :-(

https://github.com/katholt/Kaptive

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package kaptive
Release	Version	Architectures
sid	2.0.8-1	all
bookworm	2.0.4-1	all
forky	2.0.8-1	all
trixie	2.0.8-1	all
bullseye	0.7.3-3	all
upstream	3.2.1

Popcon: 7 users (37 upd.)^*

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: kaptive-data kaptive-example

Please cite: Kelly L. Wyres, Ryan R. Wick, Claire Gorrie, Adam Jenney, Rainer Follador, Nicholas R. Thomson and Kathryn E. Holt: Identification of Klebsiella capsule synthesis loci from whole genome data. (PubMed) Microbial Genomics 2(12):e000102 (2016)

Registry entries: Bioconda

khmer

??? missing short description for package khmer :-(

https://khmer.readthedocs.org

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Popcon: 0 users (0 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Michael R. Crusoe, Hussien F. Alameldin, Sherine Awad, Elmar Bucher, Adam Caldwell, Reed Cartwright, Amanda Charbonneau, Bede Constantinides, Greg Edvenson, Scott Fay, Jacob Fenton, Thomas Fenzl, Jordan Fish, Leonor Garcia-Gutierrez, Phillip Garland, Jonathan Gluck, Iván González, Sarah Guermond, Jiarong Guo, Aditi Gupta, Joshua R. Herr, Adina Howe, Alex Hyer, Andreas Härpfer, Luiz Irber, Rhys Kidd, David Lin, Justin Lippi, Tamer Mansour, Pamela McA'Nulty, Eric McDonald, Jessica Mizzi, Kevin D. Murray, Joshua R. Nahum, Kaben Nanlohy, Alexander Johan Nederbragt, Humberto Ortiz-Zuazaga, Jeramia Ory, Jason Pell, Charles Pepe-Ranney, Zachary N Russ, Erich Schwarz, Camille Scott, Josiah Seaman, Scott Sievert, Jared Simpson, Connor T. Skennerton, James Spencer, Ramakrishnan Srinivasan, Daniel Standage, James A. Stapleton, Joe Stein, Susan R Steinman, Benjamin Taylor, Will Trimble, Heather L. Wiencko, Michael Wright, Brian Wyss, Qingpeng Zhang, en zyme and C. Titus Brown: The khmer software package: enabling efficient sequence analysis. (2015)

Registry entries: Bio.tools SciCrunch Bioconda

kineticstools

??? missing short description for package kineticstools :-(

https://github.com/PacificBiosciences/kineticsTools

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package kineticstools
Release	Version	Architectures
trixie	0.6.1+git20220223.1326a4d+dfsg-6	all
bullseye	0.6.1+git20200729.e3723e0+dfsg-1	all
bookworm	0.6.1+git20220223.1326a4d+dfsg-2	all
sid	0.6.1+git20220223.1326a4d+dfsg-7	all

Popcon: 4 users (32 upd.)^*

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License: DFSG free

Official Debian package

Git

king-probe

??? missing short description for package king-probe :-(

http://kinemage.biochem.duke.edu/software/probe.php

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package king-probe
Release	Version	Architectures
trixie	02.21-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	02.21-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	2.16.160404+git20200121.9b198c1-3	amd64,arm64,armhf,i386
forky	02.21-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	02.21-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
upstream	02.26

Popcon: 76 users (19 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: J. Michael Word, Simon C. Lovell, Thomas H. LaBean, Hope C. Taylor, Michael E. Zalis, Brent K. Presley, Jane S. Richardson and David C. Richardson: Visualizing and Quantifying Molecular Goodness-of-Fit: Small-probe Contact Dots with Explicit Hydrogen Atoms. (PubMed,eprint) J. Mol. Biol. 285(4):1709-1731 (1999)

kissplice

??? missing short description for package kissplice :-(

https://kissplice.prabi.fr/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package kissplice
Release	Version	Architectures
forky	2.6.7-2	amd64,arm64,ppc64el,riscv64
sid	2.6.7-2	amd64,arm64,loong64,ppc64el,riscv64
bookworm	2.6.2-2	amd64,arm64,mips64el,ppc64el
bullseye	2.5.3-3	amd64,arm64
trixie	2.6.7-2	amd64,arm64,ppc64el,riscv64

Debtags of package kissplice:
biology	nuceleic-acids
field	biology, biology:bioinformatics
interface	commandline
role	program
use	analysing
works-with	biological-sequence

Popcon: 6 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Gustavo AT Sacomoto, Janice Kielbassa, Rayan Chikhi, Raluca Uricaru, Pavlos Antoniou, Marie-France Sagot, Pierre Peterlongo and Vincent Lacroix: KISSPLICE: de-novo calling alternative splicing events from RNA-seq data. (PubMed,eprint) BMC Bioinformatics 13((Suppl 6)):S5 (2012)

Registry entries: SciCrunch Bioconda

Topics: RNA-seq; RNA splicing; Gene structure

kleborate

??? missing short description for package kleborate :-(

https://github.com/katholt/Kleborate

Maintainer: Debian Med Packaging Team (Alexandre Detiste)

Versions of package kleborate
Release	Version	Architectures
forky	2.4.1-7	amd64,arm64,loong64,ppc64el,riscv64,s390x
bullseye	2.0.1-1	amd64,arm64
sid	2.4.1-7	amd64,arm64,loong64,ppc64el,riscv64,s390x
trixie	2.4.1-5	amd64,arm64,ppc64el,riscv64,s390x
bookworm	2.3.1-2	amd64,arm64,mips64el,ppc64el,s390x
upstream	3.2.4

Popcon: 4 users (38 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: Margaret M. C. Lam, Ryan R. Wick, Kelly L. Wyres, Claire L. Gorrie, Louise M. Judd, Adam W. J. Jenney, Sylvain Brisse and Kathryn E. Holt: Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations. (PubMed) Microbiology Society 4(9) (2018)

Registry entries: Bioconda

kma

??? missing short description for package kma :-(

https://bitbucket.org/genomicepidemiology/kma

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package kma
Release	Version	Architectures
trixie	1.4.21-1	amd64,arm64,ppc64el,riscv64,s390x
forky	1.4.21-1	amd64,arm64,loong64,ppc64el,riscv64,s390x
sid	1.4.21-1	amd64,arm64,loong64,ppc64el,riscv64,s390x
bookworm	1.4.11-1	amd64,arm64,mips64el,ppc64el,s390x
bullseye	1.3.10-1	amd64,arm64,armhf,i386
upstream	1.6.11

Popcon: 8 users (32 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Philip T. L. C. Clausen, Frank M. Aarestrup and Ole Lund: Rapid and precise alignment of raw reads against redundant databases with KMA. (PubMed,eprint) BMC Bioinformatics 19:307 (2018)

Registry entries: Bioconda

kmc

??? missing short description for package kmc :-(

https://sun.aei.polsl.pl/kmc

Maintainer: Debian Med Packaging Team (Sascha Steinbiss)

Versions of package kmc
Release	Version	Architectures
bullseye	3.1.1+dfsg-3	amd64,arm64,armhf,i386
sid	3.2.4+dfsg-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	3.2.1+dfsg-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	3.2.4+dfsg-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	3.2.4+dfsg-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

Please cite: S. Deorowicz, M. Kokot, Sz. Grabowski and A. Debudaj-Grabysz: KMC 2: Fast and resource-frugal k-mer counting. (PubMed) Bioinformatics 31(10):1569-1576 (2015)

Registry entries: Bio.tools SciCrunch Bioconda

Topics: Sequence composition, complexity and repeats

kmer

??? missing short description for package kmer :-(

http://kmer.sourceforge.net

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package kmer
Release	Version	Architectures
trixie	0~20150903+r2013-9	all
bullseye	0~20150903+r2013-8	all
bookworm	0~20150903+r2013-8	all
forky	0~20150903+r2013-10	all
sid	0~20150903+r2013-10	all

Popcon: 0 users (0 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: B. Walenz and L. Florea: Sim4db and leaff: Utilities for fast batched spliced alignment and sequence indexing. (PubMed) Bioinformatics 27(13):1869-1870 (2011)

Registry entries: Bio.tools SciCrunch Bioconda

kmerresistance

??? missing short description for package kmerresistance :-(

https://bitbucket.org/genomicepidemiology/kmerresistance

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package kmerresistance
Release	Version	Architectures
bookworm	2.2.0-4	amd64,arm64,mips64el,ppc64el,s390x
forky	2.2.0-4	amd64,arm64,loong64,ppc64el,riscv64,s390x
trixie	2.2.0-4	amd64,arm64,ppc64el,riscv64,s390x
sid	2.2.0-4	amd64,arm64,loong64,ppc64el,riscv64,s390x
bullseye	2.2.0-2	amd64,arm64,armhf,i386

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License: DFSG free

Official Debian package

Git

Please cite: Philip T. L. C. Clausen, Ea Zankari, Frank M. Aarestrup and Ole Lund: Benchmarking of methods for identification of antimicrobial resistance genes in bacterial whole genome data. (PubMed,eprint) Journal of Antimicrobial Chemotherapy 71(9):2484-8 (2016)

kraken

??? missing short description for package kraken :-(

http://ccb.jhu.edu/software/kraken/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package kraken
Release	Version	Architectures
forky	1.1.1-4	amd64,arm64,loong64,ppc64el,riscv64
trixie	1.1.1-4	amd64,arm64,ppc64el,riscv64
bookworm	1.1.1-4	amd64,arm64,mips64el,ppc64el
bullseye	1.1.1-2	amd64,arm64,armhf,i386
sid	1.1.1-4	amd64,arm64,loong64,ppc64el,riscv64

Popcon: 6 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: jellyfish1 multiqc

Please cite: Derrick E Wood and Steven L Salzberg: Kraken: ultrafast metagenomic sequence classification using exact alignments. (PubMed,eprint) Genome Biol. 15(3):R46 (2014)

Registry entries: Bio.tools Bioconda

kraken2

??? missing short description for package kraken2 :-(

https://www.ccb.jhu.edu/software/kraken2/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package kraken2
Release	Version	Architectures
bullseye	2.1.1-1	amd64,arm64,armhf,i386
trixie	2.1.3-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	2.1.3-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	2.1.3-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	2.1.2-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream	2.17.1

Popcon: 6 users (34 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: Derrick E Wood and Steven L Salzberg: Kraken: ultrafast metagenomic sequence classification using exact alignments. (PubMed,eprint) Genome Biol. 15(3):R46 (2014)

Registry entries: Bio.tools Bioconda

lagan

??? missing short description for package lagan :-(

http://lagan.stanford.edu/lagan_web/index.shtml

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package lagan
Release	Version	Architectures
bullseye	2.0-6	amd64,arm64,armhf,i386
sid	2.0-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	2.0-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	2.0-10	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	2.0-9	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 16 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Michael Brudno, Chuong Do, Gregory Cooper, Michael F. Kim, Eugene Davydov, Eric D. Green, Arend Sidow and Serafim Batzoglou: LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. (PubMed,eprint) Genome Research 13(4):721-31 (2003)

Registry entries: Bio.tools SciCrunch

lamarc

??? missing short description for package lamarc :-(

https://evolution.gs.washington.edu/lamarc/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package lamarc
Release	Version	Architectures
trixie	2.1.10.1+dfsg-7	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	2.1.10.1+dfsg-7	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	2.1.10.1+dfsg-7	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
sid	2.1.10.1+dfsg-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2.1.10.1+dfsg-5	amd64,arm64,armhf,i386

Popcon: 6 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Mary K. Kuhner: Coalescent genealogy samplers: windows into population history. (PubMed) Trends in Ecology & Evolution 24(2):86-93 (2009)

Registry entries: SciCrunch

lamassemble

??? missing short description for package lamassemble :-(

https://gitlab.com/mcfrith/lamassemble

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Popcon: 4 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

lambda-align

??? missing short description for package lambda-align :-(

https://seqan.github.io/lambda

Maintainer: Debian Med Packaging Team (Enrico Seiler)

Versions of package lambda-align
Release	Version	Architectures
bullseye	1.0.3-6	amd64,arm64,armhf,i386
bookworm	1.0.3-6	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.0.3-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	1.0.3-9	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 5 users (32 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Hannes Hauswedell, Jochen Singer and Knut Reinert: Lambda: the local aligner for massive biological data. (PubMed,eprint) Bioinformatics 30(17):i349-i355 (2014)

Registry entries: Bioconda

lambda-align2

??? missing short description for package lambda-align2 :-(

https://seqan.github.io/lambda

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package lambda-align2
Release	Version	Architectures
trixie	2.0.1-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	2.0.1-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2.0.0-9	amd64
bookworm	2.0.0-9	amd64
sid	2.0.1-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 4 users (35 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Hannes Hauswedell, Jochen Singer and Knut Reinert: Lambda: the local aligner for massive biological data. (PubMed,eprint) Bioinformatics 30(17):i349-i355 (2014)

Registry entries: Bioconda

last-align

??? missing short description for package last-align :-(

https://gitlab.com/mcfrith/last

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package last-align
Release	Version	Architectures
bullseye	1179-1	amd64,arm64,armhf,i386
forky	1651-2	amd64,arm64,loong64,ppc64el,riscv64,s390x
trixie	1609-1	amd64,arm64,ppc64el,riscv64,s390x
bookworm	1447-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1651-2	amd64,arm64,loong64,ppc64el,riscv64,s390x

Popcon: 10 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Martin C. Frith, Raymond Wan and Paul Horton: Incorporating sequence quality data into alignment improves DNA read mapping. (PubMed,eprint) Nucl. Acids Res. 38(7):e100 (2010)

Registry entries: Bio.tools SciCrunch Bioconda

lastz

??? missing short description for package lastz :-(

https://github.com/lastz/lastz

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package lastz
Release	Version	Architectures
bookworm	1.04.22-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.04.03-4	amd64,arm64,armhf,i386
trixie	1.04.22-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.04.52-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.04.52-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 4 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

leaff

??? missing short description for package leaff :-(

http://kmer.sourceforge.net

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package leaff
Release	Version	Architectures
trixie	0~20150903+r2013-9	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	0~20150903+r2013-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	0~20150903+r2013-10	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
bookworm	0~20150903+r2013-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	0~20150903+r2013-8	amd64,arm64,armhf,i386

Popcon: 4 users (42 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: B. Walenz and L. Florea: Sim4db and leaff: Utilities for fast batched spliced alignment and sequence indexing. (PubMed) Bioinformatics 27(13):1869-1870 (2011)

Registry entries: Bio.tools SciCrunch Bioconda

lefse

??? missing short description for package lefse :-(

https://github.com/SegataLab/lefse

Maintainer: Debian Med Packaging Team (Ananthu C V)

Popcon: 6 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Registry entries: SciCrunch Bioconda

libpwiz-tools

??? missing short description for package libpwiz-tools :-(

http://proteowizard.sourceforge.net/downloads.shtml

Maintainer: The Debichem Group (Adrian Bunk)

Versions of package libpwiz-tools
Release	Version	Architectures
bookworm	3.0.18342-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	3.0.18342-4	amd64,arm64,armhf,i386
sid	3.0.18342-4.2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 2 users (1 upd.)^*

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License: DFSG free

Official Debian package

Git

librg-utils-perl

??? missing short description for package librg-utils-perl :-(

https://predictprotein.org/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package librg-utils-perl
Release	Version	Architectures
sid	1.0.43-9	all
bookworm	1.0.43-8	all
forky	1.0.43-9	all
bullseye	1.0.43-7	all
trixie	1.0.43-9	all

Popcon: 4 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

libvcflib-tools

??? missing short description for package libvcflib-tools :-(

https://github.com/vcflib/vcflib

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package libvcflib-tools
Release	Version	Architectures
bookworm	1.0.3+dfsg-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.0.12+dfsg-2	amd64,arm64,loong64,ppc64el,riscv64
trixie	1.0.12+dfsg-1	amd64,arm64,ppc64el,riscv64
bullseye	1.0.2+dfsg-2	amd64,arm64,armhf,i386
upstream	1.0.15

Popcon: 6 users (34 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

lighter

??? missing short description for package lighter :-(

https://github.com/mourisl/Lighter

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package lighter
Release	Version	Architectures
bullseye	1.1.2-5	amd64,arm64,armhf,i386
trixie	1.1.3-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.1.3-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.1.3-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.1.2-7	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 4 users (34 upd.)^*

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loki

??? missing short description for package loki :-(

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package loki
Release	Version	Architectures
forky	2.4.7.4-12	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2.4.7.4-10	amd64,arm64,armhf,i386
bookworm	2.4.7.4-10	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	2.4.7.4-12	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	2.4.7.4-12	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 87 users (38 upd.)^*

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: loki-doc

ltrsift

??? missing short description for package ltrsift :-(

https://www.zbh.uni-hamburg.de/en/forschung/gi/software/ltrsift.html

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package ltrsift
Release	Version	Architectures
sid	1.0.2-11	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.0.2-9	amd64,arm64,armhf,i386
bookworm	1.0.2-9	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.0.2-10	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 5 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

lucy

??? missing short description for package lucy :-(

https://lucy.sourceforge.net

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package lucy
Release	Version	Architectures
bookworm	1.20-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	1.20-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.20-3	amd64,arm64,armhf,i386
trixie	1.20-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	1.20-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 4 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

lumpy-sv

??? missing short description for package lumpy-sv :-(

https://github.com/arq5x/lumpy-sv

Maintainer: Debian Med Packaging Team (Sudip Mukherjee)

Versions of package lumpy-sv
Release	Version	Architectures
forky	0.3.1+dfsg-8.1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
sid	0.3.1+dfsg-8.1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
bullseye	0.3.1+dfsg-5	amd64,arm64,armhf,i386
bookworm	0.3.1+dfsg-7	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el
trixie	0.3.1+dfsg-7	amd64,arm64,armel,armhf,i386,ppc64el,riscv64

Popcon: 4 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: lumpy-sv-examples

macs

??? missing short description for package macs :-(

https://github.com/taoliu/MACS/

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package macs
Release	Version	Architectures
sid	3.0.4-1	amd64,arm64,loong64,ppc64el
sid	3.0.2-3	armhf,i386,riscv64,s390x
forky	3.0.2-3	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
bullseye	2.2.7.1-3	amd64,arm64,armhf,i386
bookworm	2.2.7.1-6	amd64,arm64,armel,armhf,i386,ppc64el,s390x
trixie	3.0.2-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 9 users (35 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

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)

Registry entries: Bio.tools SciCrunch Bioconda

macsyfinder

??? missing short description for package macsyfinder :-(

https://github.com/gem-pasteur/macsyfinder

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package macsyfinder
Release	Version	Architectures
bookworm	2.0-2	amd64,i386
trixie	2.1.4-1	amd64,arm64,i386
sid	2.1.6-1	amd64,arm64,i386
bullseye	2.0~rc1-3	amd64,i386
forky	2.1.6-1	amd64,arm64,i386

Popcon: 4 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Sophie S. Abby, Bertrand Néron, Hervé Ménager, Marie Touchon and Eduardo P. C. Rocha: MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas System. (PubMed,eprint) PLOS ONE 9(10):e110726 (2014)

Registry entries: Bio.tools

maffilter

??? missing short description for package maffilter :-(

https://jydu.github.io/maffilter/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package maffilter
Release	Version	Architectures
sid	1.3.1+dfsg-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.3.1+dfsg-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.3.1+dfsg-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.3.1+dfsg-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.3.1+dfsg-2	amd64,arm64,armhf,i386

Popcon: 4 users (35 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: maffilter-examples

Please cite: Julien Y Dutheil, Sylvain Gaillard and Eva H Stukenbrock: MafFilter: a highly flexible and extensible multiple genome alignment files processor. (PubMed,eprint) BMC Genomics 15:53 (2014)

mafft

??? missing short description for package mafft :-(

https://mafft.cbrc.jp/alignment/software/

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package mafft
Release	Version	Architectures
trixie	7.505-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	7.525-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	7.475-1	amd64,arm64,armhf,i386
sid	7.525-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	7.505-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Debtags of package mafft:
biology	format:aln, nuceleic-acids, peptidic
field	biology, biology:bioinformatics
interface	commandline
role	program
scope	utility
use	comparing
works-with-format	plaintext

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License: DFSG free

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Git

Please cite: Kazutaka Katoh and Hiroyuki Toh: Recent developments in the MAFFT multiple sequence alignment program. (PubMed) Brief Bioinform 9(4):286-298 (2008)

Registry entries: Bio.tools SciCrunch Bioconda

malt

??? missing short description for package malt :-(

https://github.com/danielhuson/malt

Maintainer: Debian Med Packaging Team (Pierre Gruet)

Popcon: 5 users (31 upd.)^*

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License: DFSG free

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The package is enhanced by the following packages: multiqc

Please cite: Alexander Herbig, Frank Maixner, Kirsten I. Bos, Albert Zink, Johannes Krause and Daniel H. Huson: MALT: Fast alignment and analysis of metagenomic DNA sequence data applied to the Tyrolean Iceman. (eprint) bioRxiv (2016)

mapdamage

??? missing short description for package mapdamage :-(

https://ginolhac.github.io/mapDamage/

Maintainer: Debian Med Packaging Team (Charles Plessy)

Versions of package mapdamage
Release	Version	Architectures
bookworm	2.2.1+dfsg-3	all
trixie	2.2.2+dfsg-1	all
sid	2.2.3+dfsg-3	amd64,arm64,loong64,ppc64el,riscv64
bullseye	2.2.1+dfsg-1	all

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License: DFSG free

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Git

Please cite: Hákon Jónsson, Aurélien Ginolhac, Mikkel Schubert and Philip Johnson and Ludovic Orlando: mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. (PubMed,eprint) Bioinformatics 29(13):1682-4 (2013)

Registry entries: SciCrunch Bioconda

mapsembler2

??? missing short description for package mapsembler2 :-(

http://colibread.inria.fr/mapsembler2/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package mapsembler2
Release	Version	Architectures
bookworm	2.2.4+dfsg1-4	amd64,arm64,ppc64el,s390x
trixie	2.2.4+dfsg1-4	amd64,arm64,ppc64el,s390x
bullseye	2.2.4+dfsg1-3	amd64,arm64
sid	2.2.4+dfsg1-6	amd64,arm64,ppc64el,s390x

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License: DFSG free

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Git

Please cite: Pierre Peterlongo and Rayan Chikhi: Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer. (PubMed) BMC Bioinformatics 13:48 (2012)

Registry entries: Bio.tools Bioconda

maq

??? missing short description for package maq :-(

http://maq.sourceforge.net/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package maq
Release	Version	Architectures
bookworm	0.7.1-9	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	0.7.1-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	0.7.1-10	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	0.7.1-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	0.7.1-9	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

Popcon: 12 users (35 upd.)^*

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License: DFSG free

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Git

Please cite: Heng Li, Jue Ruan and Richard Durbin: Mapping short DNA sequencing reads and calling variants using mapping quality scores. (PubMed,eprint) Genome Research 18(11):1851-1858 (2008)

Registry entries: Bio.tools SciCrunch

maqview

??? missing short description for package maqview :-(

https://maq.sourceforge.net/maqview.shtml

Maintainer: Debian-Med Packaging Team (Étienne Mollier)

Versions of package maqview
Release	Version	Architectures
bullseye	0.2.5-10	amd64,arm64,armhf,i386
sid	0.2.5-12	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	0.2.5-11	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	0.2.5-12	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	0.2.5-12	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 7 users (34 upd.)^*

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License: DFSG free

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Git

Please cite: Heng Li, Jue Ruan and Richard Durbin: Mapping short DNA sequencing reads and calling variants using mapping quality scores. (PubMed,eprint) Genome Research 18(11):1851-1858 (2008)

Registry entries: Bio.tools SciCrunch

mash

??? missing short description for package mash :-(

https://mash.readthedocs.io

Maintainer: Debian Med Packaging Team (Sascha Steinbiss)

Versions of package mash
Release	Version	Architectures
bookworm	2.3+dfsg-3	amd64,arm64,mips64el,ppc64el,s390x
sid	2.3+dfsg-6	amd64,arm64,loong64,ppc64el,riscv64,s390x
bullseye	2.2.2+dfsg-2	amd64,arm64
trixie	2.3+dfsg-6	amd64,arm64,ppc64el,riscv64,s390x
forky	2.3+dfsg-6	amd64,arm64,loong64,ppc64el,riscv64,s390x

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License: DFSG free

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Git

Please cite: Brian D. Ondovi, Todd J. Treangen, Páll Melsted, Adam B. Mallonee, Nicholas H. Bergman, Sergey Koren and Adam M. Phillippy: Mash: fast genome and metagenome distance estimation using MinHash. (PubMed,eprint) Genome Biology 17:132 (2016)

Registry entries: Bioconda

massxpert

??? missing short description for package massxpert :-(

http://www.msxpertsuite.org/

Maintainer: The Debichem Group (Santiago Vila)

Versions of package massxpert
Release	Version	Architectures
trixie	8.5.0-2	all
bookworm	7.0.0-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	6.0.2-1	amd64,arm64,armhf,i386

Debtags of package massxpert:
biology	nuceleic-acids, peptidic
field	biology, chemistry
interface	x11
role	program
uitoolkit	qt
use	analysing, simulating
works-with	biological-sequence
works-with-format	xml
x11	application

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License: DFSG free

Official Debian package

Git

Please cite: Filippo Rusconi: massXpert 2, a cross-platform software environment for polymer chemistry modelling and simulation/analysis of mass spectrometric data. (PubMed,eprint) Bioinformatics 25(20):2741-2742 (2009)

Registry entries: Bio.tools

mauve-aligner

??? missing short description for package mauve-aligner :-(

https://darlinglab.org/mauve/

Maintainer: Debian Med Packaging Team (Pierre Gruet)

Versions of package mauve-aligner
Release	Version	Architectures
bullseye	2.4.0+4736-3	amd64,arm64,armhf,i386
bookworm	2.4.0+4736-6	all
trixie	2.4.0+4736-6	all
forky	2.4.0+4736-6	all
sid	2.4.0+4736-6	all

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License: DFSG free

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Git

The package is enhanced by the following packages: progressivemauve

Please cite: Aaron C. E. Darling, Bob Mau, Frederick R. Blattner and Nicole T. Perna: Mauve: multiple alignment of conserved genomic sequence with rearrangements. (PubMed,eprint) Genome research 14(7):1394-1403 (2004)

Registry entries: Bio.tools SciCrunch Bioconda

mcaller

??? missing short description for package mcaller :-(

https://github.com/al-mcintyre/mCaller

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package mcaller
Release	Version	Architectures
sid	1.0.3+git20210624.b415090-3	all
bookworm	1.0.3+git20210624.b415090-3	all
trixie	1.0.3+git20210624.b415090-3	all
forky	1.0.3+git20210624.b415090-3	all

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License: DFSG free

Official Debian package

Git

mecat2

??? missing short description for package mecat2 :-(

https://github.com/xiaochuanle/MECAT2

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package mecat2
Release	Version	Architectures
bookworm	0.0+git20200428.f54c542+ds-3	amd64
trixie	0.0+git20200428.f54c542+ds-4	amd64
sid	0.0+git20200428.f54c542+ds-4	amd64
forky	0.0+git20200428.f54c542+ds-4	amd64
bullseye	0.0+git20200428.f54c542+ds-3	amd64

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License: DFSG free

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Git

Please cite: Chuan-Le Xiao, Ying Chen, Shang-Qian Xie, Kai-Ning Chen, Yan Wang, Yue Han, Feng Luo and Zhi Xie: MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads. Nature Methods 14(11):1078 (2017)

megadepth

??? missing short description for package megadepth :-(

https://github.com/ChristopherWilks/megadepth

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package megadepth
Release	Version	Architectures
bookworm	1.2.0-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.2.0-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.2.0-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.2.0-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

Please cite: Christopher Wilks, Omar Ahmed, Daniel N Baker, David Zhang, Leonardo Collado-Torres and Ben Langmead: Megadepth: efficient coverage quantification for BigWigs and BAMs. (PubMed) Bioinformatics 37(18):3014–3016 (2021)

Registry entries: Bio.tools Bioconda

megahit

??? missing short description for package megahit :-(

https://github.com/voutcn/megahit

Maintainer: Debian Med Packaging Team (Pierre Gruet)

Versions of package megahit
Release	Version	Architectures
bookworm	1.2.9-4	amd64
forky	1.2.9+dfsg-1	amd64
trixie	1.2.9-5	amd64
bullseye	1.2.9-2	amd64
sid	1.2.9+dfsg-1	amd64

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License: DFSG free

Official Debian package

Git

Please cite: Dinghua Li, Chi-Man Liu, Ruibang Luo, Kunihiko Sadakane and Tak-Wah Lam: MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. (PubMed) 31:1674-1676 (2015)

Registry entries: Bio.tools Bioconda

megan-ce

??? missing short description for package megan-ce :-(

https://github.com/danielhuson/megan-ce

Maintainer: Debian Med Packaging Team (Pierre Gruet)

Popcon: 5 users (31 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Daniel H. Huson, Sina Beier, Isabell Flade, Anna Górska, Mohamed El-Hadidi, Suparna Mitra, Hans-Joachim Ruscheweyh and Rewati Tappu: MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data. (PubMed,eprint) PLoS Comput Biol. 12(6):e1004957 (2016)

Registry entries: Bioconda

melting

??? missing short description for package melting :-(

https://www.ebi.ac.uk/compneur-srv/melting/

Maintainer: Debian Med Packaging Team (Santiago Vila)

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

Popcon: 5 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Le Novère, Nicolas: MELTING, computing the melting temperature of nucleic acid duplex. (PubMed,eprint) Bioinformatics 17(12):1226-1227 (2001)

Registry entries: Bio.tools

meryl

??? missing short description for package meryl :-(

http://kmer.sourceforge.net

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package meryl
Release	Version	Architectures
bookworm	0~20150903+r2013-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	0~20150903+r2013-10	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
trixie	0~20150903+r2013-9	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	0~20150903+r2013-8	amd64,arm64,armhf,i386
sid	0~20150903+r2013-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 6 users (39 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: B. Walenz and L. Florea: Sim4db and leaff: Utilities for fast batched spliced alignment and sequence indexing. (PubMed) Bioinformatics 27(13):1869-1870 (2011)

Registry entries: Bio.tools SciCrunch Bioconda

metabat

??? missing short description for package metabat :-(

https://bitbucket.org/berkeleylab/metabat/wiki/Home

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package metabat
Release	Version	Architectures
trixie	2.15-4	amd64,i386
bullseye	2.15-3	amd64,i386
sid	2.15-4	i386
bookworm	2.15-4	amd64,i386
sid	2.18-4	amd64

Popcon: 6 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Dongwan D. Kang, Jeff Froula, Rob Egan and Zhong Wang: MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. (PubMed) PeerJ 3:e1165 (2015)

Registry entries: Bioconda

metaeuk

??? missing short description for package metaeuk :-(

https://github.com/soedinglab/metaeuk

Maintainer: Debian Med Packaging Team (Sascha Steinbiss)

Versions of package metaeuk
Release	Version	Architectures
forky	7-bba0d80+ds-2	amd64,arm64,loong64,ppc64el,riscv64
trixie	7-bba0d80+ds-1	amd64,arm64,ppc64el,riscv64
sid	7-bba0d80+ds-2	amd64,arm64,loong64,ppc64el,riscv64

Popcon: 5 users (37 upd.)^*

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License: DFSG free

Official Debian package

Git

metaphlan

??? missing short description for package metaphlan :-(

https://github.com/biobakery/MetaPhlAn

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package metaphlan
Release	Version	Architectures
trixie	4.0.4+ds-1	all
bookworm	4.0.4-1	all
sid	4.0.4+ds-1	all
forky	4.0.4+ds-1	all
upstream	4.2.4

Popcon: 8 users (33 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: Duy Tin Truong, Eric A Franzosa, Timothy L Tickle, Matthias Scholz, George Weingart, Edoardo Pasolli, Adrian Tett, Curtis Huttenhower and Nicola Segata: MetaPhlAn2 for enhanced metagenomic taxonomic profiling. (PubMed) Nature Methods 12(10):902–903 (2015)

Registry entries: Bio.tools SciCrunch Bioconda

metastudent

??? missing short description for package metastudent :-(

https://rostlab.org/owiki/index.php/Metastudent

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package metastudent
Release	Version	Architectures
bookworm	2.0.1-9	all
forky	2.0.1-10	all
bullseye	2.0.1-8	all
sid	2.0.1-10	all
trixie	2.0.1-10	all

Popcon: 8 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Tobias Hamp, Rebecca Kassner, Stefan Seemayer, Esmeralda Vicedo, Christian Schaefer, Dominik Achten, Florian Auer, Ariane Boehm, Tatjana Braun, Maximilian Hecht, Mark Heron, Peter Hönigschmid, Thomas A. Hopf, Stefanie Kaufmann, Michael Kiening, Denis Krompass, Cedric Landerer, Yannick Mahlich, Manfred Roos and Burkhard Rost: Homology-based inference sets the bar high for protein function prediction.. (PubMed) BMC Bioinformatics 14(Suppl 3):S7 (2013)

Registry entries: Bio.tools

mhap

??? missing short description for package mhap :-(

http://mhap.readthedocs.org/en/stable/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package mhap
Release	Version	Architectures
sid	2.1.3+dfsg-3	all
forky	2.1.3+dfsg-3	all
trixie	2.1.3+dfsg-3	all
bookworm	2.1.3+dfsg-3	all
bullseye	2.1.3+dfsg-3	all

Popcon: 4 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Konstantin Berlin, Sergey Koren, Chen-Shan Chin, James P Drake, Jane M Landolin and Adam M Phillippy: Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. (PubMed) Nature Biotechnology 33(6):623–630 (2015)

Registry entries: Bioconda

microbegps

??? missing short description for package microbegps :-(

http://sourceforge.net/projects/microbegps/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package microbegps
Release	Version	Architectures
sid	1.0.0-7	all
forky	1.0.0-7	all
bullseye	1.0.0-5	all
trixie	1.0.0-7	all
bookworm	1.0.0-5	all

Popcon: 6 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Martin S. Lindner and Bernhard Y. Renard: Metagenomic Profiling of Known and Unknown Microbes with MicrobeGPS. (PubMed,eprint) PLoS One 10(2):e0117711 (2015)

Registry entries: Bio.tools

microbiomeutil

??? missing short description for package microbiomeutil :-(

https://microbiomeutil.sourceforge.net/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package microbiomeutil
Release	Version	Architectures
sid	20101212+dfsg1-6	all
bullseye	20101212+dfsg1-4	all
bookworm	20101212+dfsg1-5	all
trixie	20101212+dfsg1-6	all
forky	20101212+dfsg1-6	all

Popcon: 5 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Registry entries: SciCrunch

mindthegap

??? missing short description for package mindthegap :-(

https://github.com/GATB/MindTheGap

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package mindthegap
Release	Version	Architectures
bookworm	2.3.0-2	amd64,arm64,mips64el,ppc64el
bullseye	2.2.2-2	amd64,arm64,i386
sid	2.3.0-5	amd64,arm64,loong64,ppc64el,riscv64

Popcon: 0 users (0 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools Bioconda

minexpert2

??? missing short description for package minexpert2 :-(

http://www.msxpertsuite.org/

Maintainer: The Debichem Group (Gianfranco Costamagna)

Versions of package minexpert2
Release	Version	Architectures
bookworm	8.6.3-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	11.4.2-2.1	all
sid	11.4.2-2.1	all
bullseye	7.4.1-1	amd64,arm64,armhf,i386
trixie	9.6.0-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 6 users (31 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

minia

??? missing short description for package minia :-(

http://minia.genouest.org/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package minia
Release	Version	Architectures
bookworm	3.2.6-3	amd64,arm64,mips64el,ppc64el
sid	3.2.6-5	amd64,arm64,loong64,ppc64el,riscv64
trixie	3.2.6-4	amd64,arm64,ppc64el,riscv64
forky	3.2.6-5	amd64,arm64,ppc64el,riscv64
bullseye	3.2.1+git20200522.4960a99-1	amd64,arm64,i386

Popcon: 7 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Rayan Chikhi and Guillaume Rizk: Space-Efficient and Exact de Bruijn Graph Representation Based on a Bloom Filter.. (PubMed,eprint) Algorithms for Molecular Biology 8(1):22 (2013)

Registry entries: Bio.tools SciCrunch Bioconda

Topics: Sequence assembly

miniasm

??? missing short description for package miniasm :-(

https://github.com/lh3/miniasm

Maintainer: Debian Med Packaging Team (Sascha Steinbiss)

Versions of package miniasm
Release	Version	Architectures
bookworm	0.3+dfsg-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	0.3+dfsg-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	0.3+dfsg-2	amd64,arm64,armhf,i386
forky	0.3+dfsg-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	0.3+dfsg-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 4 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Heng Li: Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. (eprint) arXiv :1512.01801 (2015)

Registry entries: Bioconda

Topics: Sequence assembly

minimac4

??? missing short description for package minimac4 :-(

https://genome.sph.umich.edu/wiki/Minimac4

Maintainer: Debian Med Packaging Team (Pierre Gruet)

Versions of package minimac4
Release	Version	Architectures
bookworm	4.1.2-1	amd64
sid	4.1.6-2	amd64
trixie	4.1.6-1	amd64
bullseye	1.0.2-2	amd64
forky	4.1.6-2	amd64

Popcon: 4 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Sayantan Das, Lukas Forer, Sebastian Schönherr, Carlo Sidore, Adam E Locke, Alan Kwong, Scott I Vrieze, Emily Y Chew, Shawn Levy, Matt McGue, David Schlessinger, Dwight Stambolian, Po-Ru Loh, William G Iacono, Anand Swaroop, Laura J Scott, Francesco Cucca, Florian Kronenberg, Michael Boehnke, Gonçalo R Abecasis and Christian Fuchsberger: Next-generation genotype imputation service and methods. Nature Genetics 48(10):1284-1287 (2016)

Registry entries: Bio.tools SciCrunch

minimap

??? missing short description for package minimap :-(

https://github.com/lh3/minimap

Maintainer: Debian Med Packaging Team (Sascha Steinbiss)

Versions of package minimap
Release	Version	Architectures
forky	0.2-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	0.2-5	amd64,arm64,armhf,i386
bookworm	0.2-7	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	0.2-8	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	0.2-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 4 users (36 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Heng Li: Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. (eprint) Bioinformatics :2103-2110 (2016)

Registry entries: Bioconda

Topics: Mapping

minimap2

??? missing short description for package minimap2 :-(

https://github.com/lh3/minimap2

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package minimap2
Release	Version	Architectures
bookworm	2.24+dfsg-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	2.27+dfsg-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	2.27+dfsg-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	2.27+dfsg-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2.17+dfsg-12	amd64,arm64,armhf,i386
upstream	2.30

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License: DFSG free

Official Debian package

Git

Please cite: Heng Li: Minimap2: pairwise alignment for nucleotide sequences. (PubMed,eprint) Bioinformatics :2103-2110 (2018)

Registry entries: Bioconda

mipe

??? missing short description for package mipe :-(

http://mipe.sourceforge.net

Maintainer: Debian Med Packaging Team (Shruti Sridhar)

Debtags of package mipe:
field	biology, biology:bioinformatics, biology:molecular
interface	commandline
role	documentation, program
scope	utility
use	organizing
works-with-format	xml

Popcon: 9 users (32 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Jan Aerts and T. Veenendaal: MIPE - a XML-format to facilitate the storage and exchange of PCR-related data. Online Journal of Bioinformatics 6(2):114-120 (2005)

Registry entries: SciCrunch

mira-assembler

??? missing short description for package mira-assembler :-(

https://sourceforge.net/p/mira-assembler/wiki/Home/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package mira-assembler
Release	Version	Architectures
trixie	4.9.6-11	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	4.9.6-7	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	4.9.6-12	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	4.9.6-12	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	4.9.6-5	amd64,arm64,armhf,i386

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License: DFSG free

Official Debian package

Git

Please cite: Bastien Chevreux, Thomas Pfisterer, Bernd Drescher, Albert J. Driesel, Werner E. G. Müller, Thomas Wetter and Sándor Suhai: Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs. (PubMed,eprint) Genome Research 14(6):1147-1159 (2004)

Registry entries: Bio.tools SciCrunch Bioconda

mirtop

??? missing short description for package mirtop :-(

https://github.com/miRTop/mirtop

Maintainer: Debian Med Packaging Team (Alexandre Detiste)

Versions of package mirtop
Release	Version	Architectures
trixie	0.4.30-1	all
bookworm	0.4.25-2	all
sid	0.4.30-1	all
forky	0.4.30-1	all
bullseye	0.4.23-2	all

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License: DFSG free

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Git

The package is enhanced by the following packages: multiqc

Please cite: Thomas Desvignes, Karen Eilbeck, Ioannis S. Vlachos, Bastian Fromm, Yin Lu, Marc K. Halushka, Michael Hackenberg, Gianvito Urgese, Elisa Ficarra, Shruthi Bandyadka, Jason Sydes, Peter Batzel, John H. Postlethwait, Phillipe Loher, Eric Londin, Aristeidis G. Telonis, Isidore Rigoutsos and Lorena Pantano Rubino: miRTOP: An open source community project for the development of a unified format file for miRNA data [version 1; not peer reviewed]. (eprint) F1000Research 7(ISCB Comm. J.):953 (Slides) (2018)

Registry entries: Bio.tools Bioconda

mlv-smile

??? missing short description for package mlv-smile :-(

http://www-igm.univ-mlv.fr/~marsan/smile_english.html

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package mlv-smile
Release	Version	Architectures
trixie	1.47-10	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	1.47-8	amd64,arm64,armhf,i386
forky	1.47-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.47-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.47-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

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License: DFSG free

Official Debian package

Git

Please cite: L. Marsan and M.-F. Sagot: Algorithms for extracting structured motifs using a suffix tree with application to promoter and regulatory site consensus identification. (PubMed,eprint) J. of Comput. Biol. 7(3-4):345-362 (2000)

mmb

??? missing short description for package mmb :-(

https://simtk.org/projects/rnatoolbox

Maintainer: Debichem Team (Andrius Merkys)

Versions of package mmb
Release	Version	Architectures
bookworm	4.0.0+dfsg-2	amd64,arm64
forky	4.2+dfsg-2	amd64,arm64,loong64,ppc64el,riscv64,s390x
experimental	4.0.0+dfsg-3.1~exp1	amd64,arm64,armhf
bullseye	3.2+dfsg-2+deb11u1	amd64,arm64
trixie	4.0.0+dfsg-5	amd64,arm64,ppc64el,riscv64,s390x
sid	4.2+dfsg-2	amd64,arm64,loong64,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

mmseqs2

??? missing short description for package mmseqs2 :-(

https://github.com/soedinglab/MMseqs2

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package mmseqs2
Release	Version	Architectures
forky	18-8cc5c+ds-1	amd64,arm64,loong64,ppc64el,riscv64
bookworm	14-7e284+ds-1	amd64,arm64,mips64el,ppc64el
trixie	15-6f452+ds-2	amd64,arm64,ppc64el,riscv64
sid	18-8cc5c+ds-1	amd64,arm64,loong64,ppc64el,riscv64
bullseye	12-113e3+ds-3	amd64,arm64,armhf,i386

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License: DFSG free

Official Debian package

Git

Please cite: Martin Steinegger and Johannes Söding: Clustering huge protein sequence sets in linear time. Nature Communications 9(1) (2018)

Registry entries: Bio.tools Bioconda

mosdepth

??? missing short description for package mosdepth :-(

https://github.com/brentp/mosdepth

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package mosdepth
Release	Version	Architectures
sid	0.3.11+ds-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
bookworm	0.3.3+ds-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el
forky	0.3.11+ds-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
bullseye	0.3.1+ds-2	amd64,arm64,armhf,i386
upstream	0.3.14

Popcon: 0 users (0 upd.)^*

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: multiqc

Please cite: Brent S Pedersen and Aaron R. Quinlan: Mosdepth: quick coverage calculation for genomes and exomes. (PubMed,eprint) Bioinformatics 34(5):867-868 (2018)

Registry entries: Bio.tools Bioconda

mothur

??? missing short description for package mothur :-(

https://www.mothur.org

Maintainer: Debian Med Packaging Team (Tomasz Buchert)

Versions of package mothur
Release	Version	Architectures
bookworm	1.48.0-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.48.5-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.48.5-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.44.3-2	amd64,arm64,armhf,i386
trixie	1.48.1-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

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)

Registry entries: Bio.tools SciCrunch Bioconda

Topics: Microbial ecology

mptp

??? missing short description for package mptp :-(

https://github.com/Pas-Kapli/mptp

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package mptp
Release	Version	Architectures
trixie	0.2.5-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	0.2.4-3	amd64,arm64,armhf,i386
sid	0.2.5-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	0.2.5-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	0.2.4-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

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License: DFSG free

Official Debian package

Git

Please cite: Paschalia Kapli, Sarah Lutteropp, Jiajie Zhang, Kassian Kobert, Pavlos Pavlidis, Alexandros Stamatakis and Tomas Flouri: Multi-rate Poisson Tree Processes for single-locus species delimitation under Maximum Likelihood and Markov Chain Monte Carlo. (PubMed,eprint) bioRxiv (2016)

mrbayes

??? missing short description for package mrbayes :-(

http://mrbayes.csit.fsu.edu/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package mrbayes
Release	Version	Architectures
bookworm	3.2.7a-6	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	3.2.7a-4	amd64,arm64,armhf,i386
trixie	3.2.7a-7	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	3.2.7a-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 9 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: mrbayes-doc

Please cite: Fredrik Ronquist, Maxim Teslenko, Paul van der Mark, Daniel L. Ayres, Aaron Darling, Sebastian Höhna, Bret Larget, Liang Liu, Marc A. Suchard and John P. Huelsenbeck: MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice across a Large Model Space. (PubMed,eprint) Systematic Biology (2012)

Registry entries: Bio.tools SciCrunch Bioconda

multiqc

??? missing short description for package multiqc :-(

https://multiqc.info/

Maintainer: Debian Med Packaging Team (Alexandre Detiste)

Versions of package multiqc
Release	Version	Architectures
trixie	1.21+dfsg-2	all
bookworm	1.14+dfsg-1	all
bullseye	1.9+dfsg-3	all
forky	1.21+dfsg-4	all
sid	1.21+dfsg-4	all
upstream	1.35

Popcon: 133 users (27 upd.)^*

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Official Debian package

Git

Please cite: Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller: MultiQC: summarize analysis results for multiple tools and samples in a single report. (PubMed,eprint) Bioinformatics 31(19):3047-8 (2016)

Registry entries: Bio.tools SciCrunch Bioconda

mummer

??? missing short description for package mummer :-(

https://mummer.sourceforge.net/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package mummer
Release	Version	Architectures
sid	3.23+dfsg-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	3.23+dfsg-7	amd64,arm64,armhf,i386
forky	3.23+dfsg-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	3.23+dfsg-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	3.23+dfsg-8	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
upstream	4.0.0.beta5

Debtags of package mummer:
field	biology, biology:bioinformatics
interface	commandline
role	program
scope	utility
use	comparing
works-with-format	plaintext

Popcon: 133 users (20 upd.)^*

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: e-mem

Please cite: Stefan Kurtz, Adam Phillippy, Arthur L. Delcher, Michael Smoot, Martin Shumway, Corina Antonescu and Steven L. Salzberg: Versatile and open software for comparing large genomes. (PubMed) Genome Biology 5(2):R12 (2004)

Registry entries: Bio.tools Bioconda

Topics: Sequence analysis

murasaki

??? missing short description for package murasaki :-(

http://murasaki.dna.bio.keio.ac.jp/wiki/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package murasaki
Release	Version	Architectures
bullseye	1.68.6-12	amd64,arm64,armhf,i386
sid	1.68.6-17	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.68.6-17	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
trixie	1.68.6-14	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.68.6-13	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 6 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Kris Popendorf, Hachiya Tsuyoshi, Yasunori Osana and Yasubumi Sakakibara: Murasaki: A Fast, Parallelizable Algorithm to Find Anchors from Multiple Genomes. (PubMed,eprint) PLOS one 5(9):e12651 (2010)

murasaki-mpi

??? missing short description for package murasaki-mpi :-(

http://murasaki.dna.bio.keio.ac.jp/wiki/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package murasaki-mpi
Release	Version	Architectures
bookworm	1.68.6-13	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.68.6-17	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.68.6-12	amd64,arm64,armhf,i386
trixie	1.68.6-14	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.68.6-17	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

muscle

??? missing short description for package muscle :-(

https://www.drive5.com/muscle/

Maintainer: Debian Med Packaging Team (Lance Lin)

Versions of package muscle
Release	Version	Architectures
forky	5.1.0-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	5.1.0-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	5.1.0-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	3.8.1551-2	amd64,arm64,armhf,i386
sid	5.1.0-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,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

Popcon: 19 users (41 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: Robert C. Edgar: MUSCLE: multiple sequence alignment with high accuracy and high throughput. (PubMed,eprint) Nucleic Acids Research 32(5):1792-1797 (2004)

Registry entries: Bio.tools SciCrunch Bioconda

Topics: Sequence analysis

muscle3

??? missing short description for package muscle3 :-(

https://www.drive5.com/muscle/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package muscle3
Release	Version	Architectures
sid	3.8.1551-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	3.8.1551-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	3.8.1551-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	3.8.1551-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 0 users (0 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Robert C. Edgar: MUSCLE: multiple sequence alignment with high accuracy and high throughput. (PubMed,eprint) Nucleic Acids Research 32(5):1792-1797 (2004)

Registry entries: Bio.tools SciCrunch Bioconda

Topics: Sequence analysis

mustang

??? missing short description for package mustang :-(

https://lcb.infotech.monash.edu.au/mustang/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package mustang
Release	Version	Architectures
bullseye	3.2.3-4	amd64,arm64,armhf,i386
sid	3.2.4-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	3.2.4-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	3.2.4-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	3.2.4-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Debtags of package mustang:
biology	peptidic
field	biology, biology:bioinformatics
interface	commandline
role	program
use	analysing, comparing
works-with-format	plaintext

Popcon: 14 users (36 upd.)^*

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License: DFSG free

Official Debian package

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The package is enhanced by the following packages: mustang-testdata

Please cite: Arun S. Konagurthu, James C. Whisstock, Peter J. Stuckey and Arthur M. Lesk: MUSTANG: A multiple structural alignment algorithm. (PubMed) Proteins: Structure, Function, and Bioinformatics 64(3):559-574 (2006)

Registry entries: Bio.tools

nanofilt

??? missing short description for package nanofilt :-(

https://github.com/wdecoster/nanofilt

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Popcon: 6 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Wouter De Coster, Svenn D'Hert, Darrin T. Schultz and Christine Van Broeckhoven: NanoPack: visualizing and processing long-read sequencing data. Bioinformatics 34 (2018)

Registry entries: Bioconda

nanolyse

??? missing short description for package nanolyse :-(

https://github.com/wdecoster/nanolyse

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package nanolyse
Release	Version	Architectures
bullseye	1.2.0-1	amd64,arm64,armhf,i386
forky	1.2.0-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.2.0-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.2.0-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.2.0-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

Please cite: Wouter De Coster, Svenn D’Hert, Darrin T Schultz, Marc Cruts and Christine Van Broeckhoven: NanoPack: visualizing and processing long-read sequencing data. (PubMed,eprint) Bioinformatics 34(15):2666-2669 (2018)

Registry entries: Bioconda

nanook

??? missing short description for package nanook :-(

https://documentation.tgac.ac.uk/display/NANOOK/NanoOK

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Popcon: 0 users (0 upd.)^*

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: nanook-examples

Please cite: Richard M. Leggett, Darren Heavens, Mario Caccamo, Matthew D. Clark and Robert P. Davey: NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles. (PubMed,eprint) Bioinformatics 32(1):142-144 (2016)

Registry entries: Bio.tools

nanopolish

??? missing short description for package nanopolish :-(

https://github.com/jts/nanopolish

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package nanopolish
Release	Version	Architectures
bookworm	0.14.0-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el
bullseye	0.13.2-3	amd64,arm64,armhf,i386
sid	0.14.0-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
forky	0.14.0-2	amd64,arm64,armhf,i386,ppc64el,riscv64
trixie	0.14.0-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64

Popcon: 8 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools SciCrunch Bioconda

nanostat

??? missing short description for package nanostat :-(

https://github.com/wdecoster/nanostat

Maintainer: Debian Med Packaging Team (Andreas Tille)

Popcon: 0 users (0 upd.)^*

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License: DFSG free

Official Debian package

Git

nanosv

??? missing short description for package nanosv :-(

https://github.com/mroosmalen/nanosv

Maintainer: Debian Med Packaging Team (Ananthu C V)

Versions of package nanosv
Release	Version	Architectures
trixie	1.2.4+git20190409.c1ae30c-7	all
bookworm	1.2.4+git20190409.c1ae30c-6	all
bullseye	1.2.4+git20190409.c1ae30c-3	all
forky	1.2.4+git20190409.c1ae30c-7	all
sid	1.2.4+git20190409.c1ae30c-7	all

Popcon: 5 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Mircea Cretu Stancu, Markus J. van Roosmalen, Ivo Renkens, Marleen M. Nieboer, Sjors Middelkamp, Joep de Ligt, Giulia Pregno, Daniela Giachino, Giorgia Mandrile, Jose Espejo Valle-Inclan, Jerome Korzelius, Ewart de Bruijn, Edwin Cuppen, Michael E. Talkowski, Tobias Marschall, Jeroen de Ridder and Wigard P. Kloosterman: Mapping and phasing of structural variation in patient genomes using nanopore sequencing.. (eprint) Nature Communications 8:1326 (2017)

Registry entries: Bioconda

nast-ier

??? missing short description for package nast-ier :-(

https://microbiomeutil.sourceforge.net/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package nast-ier
Release	Version	Architectures
forky	20101212+dfsg1-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	20101212+dfsg1-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	20101212+dfsg1-5	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	20101212+dfsg1-4	amd64,arm64,armhf,i386
sid	20101212+dfsg1-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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Git

The package is enhanced by the following packages: microbiomeutil-data

Registry entries: SciCrunch

ncbi-acc-download

??? missing short description for package ncbi-acc-download :-(

https://github.com/kblin/ncbi-acc-download

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package ncbi-acc-download
Release	Version	Architectures
bookworm	0.2.8-1	all
forky	0.2.8-3	all
bullseye	0.2.7-1	all
trixie	0.2.8-3	all
sid	0.2.8-3	all
upstream	0.2.9

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Git

Registry entries: Bioconda

ncbi-blast+

??? missing short description for package ncbi-blast+ :-(

https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/

Maintainer: Debian Med Packaging Team (Aaron M. Ucko)

Versions of package ncbi-blast+
Release	Version	Architectures
sid	2.17.0+ds-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2.11.0+ds-1	amd64,arm64,armhf,i386
forky	2.17.0+ds-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	2.12.0+ds-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	2.16.0+ds-7	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

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Registry entries: Bio.tools SciCrunch Bioconda

ncbi-blast+-legacy

??? missing short description for package ncbi-blast+-legacy :-(

https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/

Maintainer: Debian Med Packaging Team (Aaron M. Ucko)

Versions of package ncbi-blast+-legacy
Release	Version	Architectures
trixie	2.16.0+ds-7	all
sid	2.17.0+ds-7	all
forky	2.17.0+ds-7	all
bookworm	2.12.0+ds-3	all
bullseye	2.11.0+ds-1	all

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License: DFSG free

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Git

Registry entries: Bio.tools SciCrunch Bioconda

ncbi-entrez-direct

??? missing short description for package ncbi-entrez-direct :-(

http://www.ncbi.nlm.nih.gov/books/NBK179288

Maintainer: Debian Med Packaging Team (Aaron M. Ucko)

Versions of package ncbi-entrez-direct
Release	Version	Architectures
trixie	24.0.20250523+dfsg-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	19.0.20230216+dfsg-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	24.0.20250523+dfsg-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	14.6.20210224+dfsg-4	amd64,arm64,armhf,i386
forky	24.0.20250523+dfsg-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
upstream	25.5.20260512

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ncbi-epcr

??? missing short description for package ncbi-epcr :-(

https://www.ncbi.nlm.nih.gov/tools/epcr/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package ncbi-epcr
Release	Version	Architectures
bullseye	2.3.12-1-9	amd64,arm64,armhf,i386
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,ppc64el,riscv64,s390x
forky	2.3.12-1-11	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	2.3.12-1-11	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Debtags of package ncbi-epcr:
field	biology, biology:bioinformatics
interface	commandline
role	program
scope	utility
use	checking, searching
works-with-format	plaintext

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Please cite: Gregory D. Schuler: Sequence Mapping by Electronic PCR. (PubMed,eprint) Genome Research 7(5):541-550 (1997)

Registry entries: Bioconda

ncbi-seg

??? missing short description for package ncbi-seg :-(

https://ftp.ncbi.nih.gov/pub/seg/seg/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package ncbi-seg
Release	Version	Architectures
bookworm	0.0.20000620-6	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	0.0.20000620-7	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	0.0.20000620-6	amd64,arm64,armhf,i386
sid	0.0.20000620-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	0.0.20000620-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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Please cite: John C. Wootton and Scott Federhen: Statistics of local complexity in amino acid sequences and sequence databases.. Computers & Chemistry 17:149-163 (1993)

ncbi-tools-bin

??? missing short description for package ncbi-tools-bin :-(

https://www.ncbi.nlm.nih.gov/IEB/ToolBox/

Maintainer: Debian Med Packaging Team (Aaron M. Ucko)

Versions of package ncbi-tools-bin
Release	Version	Architectures
bullseye	6.1.20170106+dfsg1-9	amd64,arm64,armhf,i386
sid	6.1.20170106+dfsg2-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	6.1.20170106+dfsg2-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	6.1.20170106+dfsg1-10	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	6.1.20170106+dfsg2-7	amd64,arm64,armhf,i386,loong64,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

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The package is enhanced by the following packages: mcl

Registry entries: Bio.tools SciCrunch

ncbi-tools-x11

??? missing short description for package ncbi-tools-x11 :-(

https://www.ncbi.nlm.nih.gov/IEB/ToolBox/

Maintainer: Debian Med Packaging Team (Aaron M. Ucko)

Versions of package ncbi-tools-x11
Release	Version	Architectures
forky	6.1.20170106+dfsg2-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	6.1.20170106+dfsg2-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	6.1.20170106+dfsg1-9	amd64,arm64,armhf,i386
bookworm	6.1.20170106+dfsg1-10	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	6.1.20170106+dfsg2-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Debtags of package ncbi-tools-x11:
biology	nuceleic-acids, peptidic
field	biology, biology:bioinformatics, biology:structural
interface	3d, x11
network	client
role	program
science	visualisation
scope	utility
uitoolkit	motif
use	analysing, calculating, editing, searching, viewing
x11	application

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Registry entries: Bio.tools SciCrunch

ncl-tools

??? missing short description for package ncl-tools :-(

https://github.com/mtholder/ncl

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package ncl-tools
Release	Version	Architectures
sid	2.1.21+git20210811.b1213a7-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	2.1.21+git20210811.b1213a7-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	2.1.21+git20210811.b1213a7-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	2.1.21+git20210811.b1213a7-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	2.1.21+git20190531.feceb81-3	amd64,arm64,armhf,i386
upstream	2.1.21+git20260129.64db8d9

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Git

Please cite: Paul O. Lewis: NCL: a C++ class library for interpreting data files in NEXUS format. (PubMed,eprint) Bioinformatics 19(17):2330-2331 (2003)

ncoils

??? missing short description for package ncoils :-(

http://www.russelllab.org/coils/

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package ncoils
Release	Version	Architectures
trixie	2002-9	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	2002-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	2002-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	2002-9	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	2002-8	amd64,arm64,armhf,i386

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Git

Please cite: Andrei Lupas, Marc Van Dyke and Jeff Stock: Predicting coiled coils from protein sequences. (PubMed) Science 252:1162-1164 (1991)

Registry entries: Bio.tools SciCrunch

neobio

??? missing short description for package neobio :-(

http://neobio.sourceforge.net/

Maintainer: Debian Med Packaging Team (tony mancill)

Versions of package neobio
Release	Version	Architectures
forky	0.0.20030929-6	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

Popcon: 4 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Maxime Crochemore, Gad M. Landau and Michal Ziv-Ukelson: A sub-quadratic sequence alignment algorithm for unrestricted cost matrices. :679-688 (2002)

Registry entries: Bio.tools

ngmlr

??? missing short description for package ngmlr :-(

https://github.com/philres/ngmlr

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package ngmlr
Release	Version	Architectures
forky	0.2.7+git20210816.a2a31fb+dfsg-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	0.2.7+git20210816.a2a31fb+dfsg-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	0.2.7+git20210816.a2a31fb+dfsg-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	0.2.7+dfsg-4	amd64,arm64,armhf,i386
sid	0.2.7+git20210816.a2a31fb+dfsg-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

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Git

Please cite: Fritz J. Sedlazeck, Philipp Rescheneder, Moritz Smolka, Han Fang, Maria Nattestad, Arndt von Haeseler and Michael C. Schatz: Accurate detection of complex structural variations using single-molecule sequencing. Nature Methods 15:461–468 (2018)

Registry entries: Bio.tools SciCrunch Bioconda

njplot

??? missing short description for package njplot :-(

https://pbil.univ-lyon1.fr/software/njplot

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package njplot
Release	Version	Architectures
trixie	2.4-9	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	2.4-9	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	2.4-9	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	2.4-9	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2.4-9	amd64,arm64,armhf,i386

Debtags of package njplot:
field	biology, biology:bioinformatics
interface	x11
role	program
scope	utility
uitoolkit	motif
use	analysing, editing, organizing, printing, viewing
works-with	biological-sequence
works-with-format	plaintext
x11	application

Popcon: 9 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: G. Perrière and M. Gouy: WWW-query: An on-line retrieval system for biological sequence banks. (PubMed) Biochimie 78(5):364–369 (1996)

Registry entries: Bio.tools

norsnet

??? missing short description for package norsnet :-(

https://www.rostlab.org/owiki/index.php/Norsnet

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package norsnet
Release	Version	Architectures
trixie	1.0.17-7	all
forky	1.0.17-8	all
bullseye	1.0.17-6	all
bookworm	1.0.17-7	all
sid	1.0.17-8	all

Popcon: 5 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Avner Schlessinger, Jinfeng Liu and Burkhard Rost: Natively unstructured loops differ from other loops.. (PubMed,eprint) PLoS Comput Biol. 3:e140 (2007)

Registry entries: Bio.tools

norsp

??? missing short description for package norsp :-(

https://rostlab.org/owiki/index.php/NORSp_-_predictor_of_NOn-Regular_Secondary_Structure

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Popcon: 6 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Jinfeng Liu and Burkhard Rost: NORSp: Predictions of long regions without regular secondary structure.. (PubMed,eprint) Nucleic Acids Res 31(13):3833-3835 (2003)

Registry entries: Bio.tools

ntcard

??? missing short description for package ntcard :-(

https://github.com/bcgsc/ntCard

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package ntcard
Release	Version	Architectures
bookworm	1.2.2+dfsg-5	amd64,arm64,mips64el,ppc64el
sid	1.2.2+dfsg-10	amd64,arm64,loong64,ppc64el,riscv64,s390x
forky	1.2.2+dfsg-10	amd64,arm64,loong64,ppc64el,riscv64,s390x
trixie	1.2.2+dfsg-9	amd64,arm64,ppc64el,riscv64,s390x

Popcon: 5 users (33 upd.)^*

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License: DFSG free

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Git

Please cite: Hamid Mohamadi, Hamza Khan and Inanc Birol: ntCard: a streaming algorithm for cardinality estimation in genomics data. (PubMed,eprint) Bioinformatics 33(9):1324-1330 (2017)

Registry entries: Bio.tools Bioconda

nxtrim

??? missing short description for package nxtrim :-(

https://github.com/sequencing/NxTrim

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package nxtrim
Release	Version	Architectures
bookworm	0.4.3+dfsg-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	0.4.3+dfsg-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	0.4.3+dfsg-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	0.4.3+dfsg-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 4 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools Bioconda

obitools

??? missing short description for package obitools :-(

https://metabarcoding.org/obitools3

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package obitools
Release	Version	Architectures
forky	3.0.1~b26+dfsg-5	amd64,arm64,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.2.13+dfsg-5	amd64
sid	3.0.1~b26+dfsg-5	amd64,arm64,i386,loong64,ppc64el,riscv64,s390x
trixie	3.0.1~b26+dfsg-4	amd64,arm64,i386,ppc64el,riscv64,s390x
bullseye	1.2.13+dfsg-3	amd64

Popcon: 8 users (31 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Frédéric Boyer, Céline Mercier, Aurélie Bonin, Yvan Le Bras, Pierre Taberlet and Eric Coissac: obitools: a unix-inspired software package for DNA metabarcoding.. (PubMed,eprint) Mol. Ecol. Resour. 16(1):176-182 (2016)

Registry entries: Bio.tools Bioconda

openms

??? missing short description for package openms :-(

https://www.openms.de

Maintainer: The Debichem Group (Santiago Vila)

Versions of package openms
Release	Version	Architectures
sid	2.6.0+cleaned1-6	all
bullseye	2.6.0+cleaned1-3	all
bookworm	2.6.0+cleaned1-3	all
trixie	2.6.0+cleaned1-4	all
forky	2.6.0+cleaned1-6	all
upstream	2.9.1

Popcon: 0 users (0 upd.)^*

License: DFSG free

Official Debian package

Git

Please cite: Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert and Oliver Kohlbacher: OpenMS – an Open-Source Software Framework for Mass Spectrometry. (PubMed,eprint) BMC Bioinformatics 9(163) (2008)

Registry entries: Bio.tools SciCrunch Bioconda

optimir

??? missing short description for package optimir :-(

https://github.com/FlorianThibord/OptimiR

Maintainer: Debian Med Packaging Team (Alexandre Detiste)

Popcon: 6 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Florian Thibord, Claire Perret, Maguelonne Roux, Pierre Suchon, Marine Germain, Jean-François Deleuze, Pierre-Emmanuel Morange and David-Alexandre Trégouët: OPTIMIR, a novel algorithm for integrating available genome-wide genotype data into miRNA sequence alignment analysis. RNA (2019)

Registry entries: Bio.tools Bioconda

pal2nal

??? missing short description for package pal2nal :-(

http://www.bork.embl.de/pal2nal

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Popcon: 6 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Mikita Suyama, David Torrents and Peer Bork: PAL2NAL: robust conversion of protein sequence alignment into the corresponding codon alignments. (PubMed,eprint) Nucleic Acids Research 34:W609-W612 (2006)

Registry entries: Bio.tools Bioconda

paleomix

??? missing short description for package paleomix :-(

https://geogenetics.ku.dk/publications/paleomix

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package paleomix
Release	Version	Architectures
trixie	1.3.8-2	amd64,arm64
sid	1.3.10-1	amd64,arm64
bookworm	1.3.7-3	amd64,arm64
bullseye	1.3.2-1	amd64,arm64
upstream	1.4.0

Popcon: 4 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Mikkel Schubert, Luca Ermini, Clio Der Sarkissian, Hákon Jónsson, Aurélien Ginolhac, Robert Schaefer, Michael D Martin, Ruth Fernández, Martin Kircher, Molly McCue, Eske Willerslev and Ludovic Orlando: Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. (PubMed) Nature Protocols 9(5):1056-82 (2014)

Registry entries: Bio.tools SciCrunch

paml

??? missing short description for package paml :-(

http://abacus.gene.ucl.ac.uk/software/paml.html

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package paml
Release	Version	Architectures
sid	4.9j+dfsg-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	4.9j+dfsg-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	4.9j+dfsg-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	4.9j+dfsg-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	4.9j+dfsg-3	amd64,arm64,armhf,i386

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License: DFSG free

Official Debian package

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Please cite: Ziheng Yang: PAML 4: phylogenetic analysis by maximum likelihood. (PubMed,eprint) Molecular Biology and Evolution 24(8):1586-91 (2007)

Registry entries: Bio.tools SciCrunch Bioconda

paraclu

??? missing short description for package paraclu :-(

https://gitlab.com/mcfrith/paraclu

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package paraclu
Release	Version	Architectures
forky	10-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	10-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	10-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	10-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	9-3	amd64,arm64,armhf,i386

Popcon: 6 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Martin C. Frith, Eivind Valen, Anders Krogh, Yoshihide Hayashizaki, Piero Carninci and Albin Sandelin: A code for transcription initiation in mammalian genomes. (eprint) Genome Research 18(1):1-12 (2008)

parasail

??? missing short description for package parasail :-(

https://github.com/jeffdaily/parasail

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package parasail
Release	Version	Architectures
bullseye	2.4.3+dfsg-2	amd64,arm64,armhf,i386
sid	2.6.2+dfsg-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	2.6.2+dfsg-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	2.6.2+dfsg-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	2.6+dfsg-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 6 users (37 upd.)^*

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License: DFSG free

Official Debian package

Git

parsinsert

??? missing short description for package parsinsert :-(

http://sourceforge.net/projects/parsinsert/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package parsinsert
Release	Version	Architectures
bookworm	1.04-12	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	1.04-17	amd64,arm64,i386,loong64,ppc64el,riscv64,s390x
trixie	1.04-15	amd64,arm64,i386,ppc64el,riscv64,s390x
sid	1.04-17	amd64,arm64,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.04-10	amd64,arm64,armhf,i386

Popcon: 5 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: parsinsert-testdata

parsnp

??? missing short description for package parsnp :-(

https://harvest.readthedocs.org/en/latest/content/parsnp.html

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package parsnp
Release	Version	Architectures
bookworm	1.7.4+dfsg-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	2.1.3+dfsg-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	2.1.3+dfsg-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	2.1.3+dfsg-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.5.4+dfsg-1	amd64,arm64,armhf,i386
upstream	2.1.5

Popcon: 6 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Todd J. Treangen, Brian D. Ondov, Sergey Koren and Adam M. Phillippy: The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. (PubMed,eprint) Genome Biology 15(11):524 (2014)

Registry entries: Bioconda

patman

??? missing short description for package patman :-(

https://bioinf.eva.mpg.de/patman/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package patman
Release	Version	Architectures
trixie	1.2.2+dfsg-8	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	1.2.2+dfsg-7	amd64,arm64,armhf,i386
bookworm	1.2.2+dfsg-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	1.2.2+dfsg-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.2.2+dfsg-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 5 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Kay Prüfer, Udo Stenzel, Michael Dannemann, Richard E Green, Michael Lachmann and Janet Kelso: PatMaN: rapid alignment of short sequences to large databases. (PubMed,eprint) Bioinformatics 24(13):1530-1 (2008)

Registry entries: Bio.tools SciCrunch

pbdagcon

??? missing short description for package pbdagcon :-(

https://github.com/PacificBiosciences/pbdagcon

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package pbdagcon
Release	Version	Architectures
sid	0.3+git20180411.c14c422+dfsg-10	amd64,arm64,loong64,ppc64el,riscv64
bullseye	0.3+git20180411.c14c422+dfsg-1	amd64,arm64
bookworm	0.3+git20180411.c14c422+dfsg-8	amd64,arm64,mips64el,ppc64el
forky	0.3+git20180411.c14c422+dfsg-10	amd64,arm64,ppc64el,riscv64
trixie	0.3+git20180411.c14c422+dfsg-9	amd64,arm64,ppc64el,riscv64

Popcon: 6 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

pbhoney

??? missing short description for package pbhoney :-(

http://sourceforge.net/projects/pb-jelly

Maintainer: Debian Med Packaging Team (Andreas Tille)

Popcon: 0 users (0 upd.)^*

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License: DFSG free

Official Debian package

Git

pbjelly

??? missing short description for package pbjelly :-(

http://sourceforge.net/projects/pb-jelly

Maintainer: Debian Med Packaging Team (Andreas Tille)

Popcon: 0 users (0 upd.)^*

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License: DFSG free

Official Debian package

Git

pbsim

??? missing short description for package pbsim :-(

https://github.com/pfaucon/PBSIM-PacBio-Simulator

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package pbsim
Release	Version	Architectures
trixie	1.0.3+git20180330.e014b1d+dfsg-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	1.0.3+git20180330.e014b1d+dfsg-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.0.3+git20180330.e014b1d+dfsg-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	1.0.3+git20180330.e014b1d+dfsg-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.0.3+git20180330.e014b1d+dfsg-2	amd64,arm64,armhf,i386

Popcon: 5 users (33 upd.)^*

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Please cite: Yukiteru Ono, Kiyoshi Asai and Michiaki Hamada: PBSIM: PacBio reads simulator - toward accurate genome assembly. (PubMed,eprint) Bioinformatics 29(1):119-121 (2013)

Registry entries: Bio.tools SciCrunch Bioconda

Topics: Sequence analysis

pbsuite

??? missing short description for package pbsuite :-(

http://sourceforge.net/projects/pb-jelly

Maintainer: Debian Med Packaging Team (Andreas Tille)

Popcon: 0 users (0 upd.)^*

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License: DFSG free

Official Debian package

Git

pdb2pqr

??? missing short description for package pdb2pqr :-(

https://www.poissonboltzmann.org

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package pdb2pqr
Release	Version	Architectures
bookworm	3.5.2+dfsg-3	all
bullseye	2.1.1+dfsg-7+deb11u1	amd64,arm64,armhf,i386
trixie	3.6.1+dfsg-1	all
forky	3.6.1+dfsg-2	all
sid	3.6.1+dfsg-2	all
upstream	3.7.1

Popcon: 17 users (33 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: Todd J Dolinsky, Paul Czodrowski, Hui Li, Jens E Nielsen, Jan H Jensen, Gerhard Klebe and Nathan A Baker: PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. (PubMed,eprint) Nucleic Acids Research 35:W522-5 (2007)

perlprimer

??? missing short description for package perlprimer :-(

http://perlprimer.sourceforge.net

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package perlprimer
Release	Version	Architectures
trixie	1.2.4-2	all
forky	1.2.4-2	all
sid	1.2.4-2	all
bullseye	1.2.4-2	all
bookworm	1.2.4-2	all

Debtags of package perlprimer:
biology	format:aln, nuceleic-acids, peptidic
field	biology, biology:molecular
interface	x11
network	client
role	program
scope	utility
uitoolkit	tk
use	analysing
works-with-format	plaintext
x11	application

Popcon: 6 users (32 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Owen J. Marshall: PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR. (PubMed,eprint) Bioinformatics 20(15):2471-2472 (2004)

Registry entries: SciCrunch

perm

??? missing short description for package perm :-(

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package perm
Release	Version	Architectures
forky	0.4.0-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	0.4.0-8	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	0.4.0-7	amd64,arm64,armhf,i386
sid	0.4.0-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	0.4.0-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 5 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Yangho Chen, Tade Souaiaia and Ting Chen: PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. (PubMed,eprint) Bioinformatics 25(19):2514-21 (2009)

Registry entries: Bio.tools SciCrunch

pftools

??? missing short description for package pftools :-(

https://github.com/sib-swiss/pftools3

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package pftools
Release	Version	Architectures
forky	3.2.12-3	amd64
sid	3.2.12-3	amd64
trixie	3.2.12-1	amd64
bookworm	3.2.12-1	amd64
bullseye	3.2.6-1	amd64
upstream	3.2.13

Popcon: 17 users (32 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: Christian J. A. Sigrist, Lorenzo Cerutti, Nicolas Hulo, Alexandre Gattiker, Laurent Falquet, Marco Pagni, Amos Bairoch and Philipp Bucher: PROSITE: a documented database using patterns and profiles as motif descriptors. (PubMed,eprint) Briefings in Bioinformatics 3(3):265-74 (2002)

Registry entries: Bio.tools

phast

??? missing short description for package phast :-(

http://compgen.cshl.edu/phast/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package phast
Release	Version	Architectures
sid	1.8+dfsg-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.5+dfsg-2	amd64,arm64,armhf,i386
bookworm	1.6+dfsg-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.7+dfsg-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.8+dfsg-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
upstream	1.9.7

Popcon: 10 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Melissa J. Hubisz, Katherine S. Pollard and Adam Siepel: PHAST and RPHAST: phylogenetic analysis with space/time models. (PubMed,eprint) Bioinformatics 12(1):41-51 (2011)

Registry entries: SciCrunch Bioconda

phipack

??? missing short description for package phipack :-(

https://www.maths.otago.ac.nz/~dbryant/software/phimanual.pdf

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package phipack
Release	Version	Architectures
trixie	0.0.20160614-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	0.0.20160614-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	0.0.20160614-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	0.0.20160614-5	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	0.0.20160614-5	amd64,arm64,armhf,i386

Popcon: 4 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Trevor C. Bruen, Hervé Philippe and David Bryant: A Simple and Robust Statistical Test for Detecting the Presence of Recombination. (PubMed,eprint) Genetics 172(4):2665-2681 (2006)

Registry entries: Bioconda

phybin

??? missing short description for package phybin :-(

https://www.cs.indiana.edu/~rrnewton/projects/phybin/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package phybin
Release	Version	Architectures
forky	0.3-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	0.3-6	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	0.3-5	amd64,arm64,armhf,i386
sid	0.3-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	0.3-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 4 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Ryan R. Newton and Irene L.G. Newton: PhyBin: binning trees by topology. (PubMed,eprint) PeerJ 1:e187 (2013)

phylip

??? missing short description for package phylip :-(

https://evolution.genetics.washington.edu/phylip.html

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package phylip
Release	Version	Architectures
bookworm	3.697+dfsg-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	3.697+dfsg-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	3.697+dfsg-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	3.697+dfsg-2	amd64,arm64,armhf,i386
trixie	3.697+dfsg-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
upstream	3.698

Debtags of package phylip:
field	biology, biology:bioinformatics
interface	commandline
role	program
scope	utility
use	analysing, comparing
works-with-format	plaintext

Popcon: 15 users (37 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools SciCrunch Bioconda

phylonium

??? missing short description for package phylonium :-(

https://github.com/EvolBioInf/phylonium

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package phylonium
Release	Version	Architectures
trixie	1.7-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.6-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.3-1	amd64,arm64,armhf,i386
forky	1.7-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.7-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 5 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Topics: Phylogenetics

phyml

??? missing short description for package phyml :-(

http://www.atgc-montpellier.fr/phyml

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package phyml
Release	Version	Architectures
sid	3.3.20250515-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	3.3.20200621-1	amd64,arm64,armhf,i386
bookworm	3.3.20220408-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	3.3.20250515-2	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
trixie	3.3.20220408-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Debtags of package phyml:
biology	peptidic
field	biology, biology:bioinformatics
interface	commandline
role	program
use	analysing, comparing
works-with	biological-sequence

Popcon: 14 users (38 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Stéphane Guindon: Bayesian estimation of divergence times from large sequence alignments. (PubMed,eprint) Molecular Biology and Evolution 27(8):1768-81 (2010)

Registry entries: Bio.tools SciCrunch Bioconda

physamp

??? missing short description for package physamp :-(

https://jydu.github.io/physamp/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package physamp
Release	Version	Architectures
bookworm	1.1.0-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.1.0-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.1.0-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.1.0-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.1.0-2	amd64,arm64,armhf,i386
upstream	1.2.0

Popcon: 5 users (33 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: Julien Y. Dutheil and Emeric Figuet: Optimization of sequence alignments according to the number of sequences vs. number of sites trade-off. (PubMed,eprint) BMC Bioinformatics 16:160 (2015)

phyutility

??? missing short description for package phyutility :-(

https://github.com/blackrim/phyutility

Maintainer: Debian Med Packaging Team (Andreas Tille)

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,ppc64el,riscv64,s390x
forky	2.7.3+dfsg-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	2.7.3+dfsg-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2.7.3+dfsg-3	amd64,arm64,armhf,i386

Popcon: 8 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Stephen A. Smith and Casey W. Dunn: Phyutility: a phyloinformatics utility for trees, alignments, and molecular data. (PubMed,eprint) Bioinformatics 24(5):715-716 (2008)

phyx

??? missing short description for package phyx :-(

https://github.com/FePhyFoFum/phyx

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package phyx
Release	Version	Architectures
bullseye	1.01+ds-2+deb11u1	amd64,arm64,armhf,i386
bookworm	1.3+ds-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.3.2+ds-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.3.2+ds-1	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
sid	1.3.2+ds-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 8 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

picard-tools

??? missing short description for package picard-tools :-(

https://broadinstitute.github.io/picard/

Maintainer: Debian Med Packaging Team (Pierre Gruet)

Versions of package picard-tools
Release	Version	Architectures
bookworm	2.27.5+dfsg-2	all
trixie	3.3.0+dfsg-2	all
forky	3.4.0+dfsg-1	all
sid	3.4.0+dfsg-1	all
bullseye	2.24.1+dfsg-1	all

Popcon: 10 users (35 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: multiqc

Please cite: Broad Institute: Picard toolkit. Broad Institute, GitHub repository (2019)

Registry entries: Bio.tools SciCrunch Bioconda

Topics: Sequencing; Document, record and content management

picopore

??? missing short description for package picopore :-(

https://github.com/scottgigante/picopore

Maintainer: Debian Med Packaging Team (Andreas Tille)

Popcon: 7 users (32 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Scott Gigante: Picopore: A tool for reducing the storage size of Oxford Nanopore Technologies datasets without loss of functionality. (PubMed,eprint) F1000Res 6:227 (2017)

Registry entries: Bio.tools Bioconda

pigx-rnaseq

??? missing short description for package pigx-rnaseq :-(

https://github.com/BIMSBbioinfo/pigx_rnaseq

Maintainer: Debian Med Packaging Team (Santiago Vila)

Popcon: 3 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Ricardo Wurmus, Bora Uyar, Brendan Osberg, Vedran Franke, Alexander Gosdschan, Katarzyna Wreczycka, Jonathan Ronen and and Altuna Akalin: PiGx: Reproducible Genomics Analysis Pipelines with GNU Guix. (PubMed,eprint) GigaScience 7(12):giy123 (2018)

Registry entries: SciCrunch

piler

??? missing short description for package piler :-(

https://www.drive5.com/piler/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package piler
Release	Version	Architectures
forky	0~20140707-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	0~20140707-3	amd64,arm64,armhf,i386
bookworm	0~20140707-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	0~20140707-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	0~20140707-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 6 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Robert C. Edgar and Eugene W. Myers: PILER: identification and classification of genomic repeats. (PubMed,eprint) Bioinformatics 21(suppl 1):i152-i158 (2005)

Registry entries: Bioconda

pilercr

??? missing short description for package pilercr :-(

https://www.drive5.com/pilercr/

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package pilercr
Release	Version	Architectures
bullseye	1.06+dfsg-4	amd64,arm64,armhf,i386
trixie	1.06+dfsg-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.06+dfsg-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.06+dfsg-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.06+dfsg-5	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 4 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: R. C. Edgar: PILER-CR: fast and accurate identification of CRISPR repeats. (PubMed,eprint) BMC Bioinformatics 8:18 (2007)

pilon

??? missing short description for package pilon :-(

https://github.com/broadinstitute/pilon/wiki

Maintainer: Debian Med Packaging Team (Pierre Gruet)

Popcon: 5 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Bruce J. Walker, Thomas Abeel, Terrance Shea, Margaret Priest, Amr Abouelliel, Sharadha Sakthikumar, Christina A. Cuomo, Qiandong Zeng, Jennifer Wortman, Sarah K. Young and Ashlee M. Earl: Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement". (PubMed,eprint) PLOSone 9(11):e11296 (2014)

Registry entries: Bio.tools SciCrunch Bioconda

pinfish

??? missing short description for package pinfish :-(

https://github.com/nanoporetech/pinfish

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package pinfish
Release	Version	Architectures
sid	0.1.0+ds-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	0.1.0+ds-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	0.1.0+ds-3	amd64,arm64,mips64el,ppc64el,s390x
bullseye	0.1.0+ds-2	amd64,arm64
forky	0.1.0+ds-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

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pique

??? missing short description for package pique :-(

https://github.com/tony-travis/PIQUE/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

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License: DFSG free

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Git

The package is enhanced by the following packages: pique-doc

pirs

??? missing short description for package pirs :-(

https://github.com/galaxy001/pirs

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package pirs
Release	Version	Architectures
forky	2.0.2+dfsg-13	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
sid	2.0.2+dfsg-13	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2.0.2+dfsg-9	amd64,arm64,armhf,i386
bookworm	2.0.2+dfsg-11	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	2.0.2+dfsg-12	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

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Please cite: Xuesong Hu, Jianying Yuan, Yujian Shi, Jianliang Lu, Binghang Liu, Zhenyu Li, Yanxiang Chen, Desheng Mu, Hao Zhang, Nan Li, Zhen Yue, Fan Bai, Heng Li and Wei Fan: pIRS: Profile-based Illumina pair-end reads simulator. (PubMed,eprint) Bioinformatics 28(11):1533-5 (2012)

Registry entries: Bioconda

pizzly

??? missing short description for package pizzly :-(

https://github.com/pmelsted/pizzly

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package pizzly
Release	Version	Architectures
trixie	0.37.3+ds-9	amd64,arm64,ppc64el,riscv64,s390x
sid	0.37.3+ds-12	amd64,arm64,loong64,ppc64el,riscv64,s390x
bookworm	0.37.3+ds-9	amd64,arm64,mips64el,ppc64el,s390x
bullseye	0.37.3+ds-5	amd64,arm64,armhf,i386

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License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

placnet

??? missing short description for package placnet :-(

http://sourceforge.net/projects/placnet/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Popcon: 3 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Val F. Lanza, María de Toro, M. Pilar Garcillán-Barcia, Azucena Mora, Jorge Blanco, Teresa M. Coque and Fernando de la Cruz: Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences. (PubMed,eprint) PLOS 10(12):e1004766 (2014)

plasmidid

??? missing short description for package plasmidid :-(

https://github.com/BU-ISCIII/plasmidID

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package plasmidid
Release	Version	Architectures
forky	1.6.5+dfsg-2	amd64,arm64
trixie	1.6.5+dfsg-2	amd64,arm64
bookworm	1.6.5+dfsg-2	amd64
sid	1.6.5+dfsg-2	amd64,arm64
bullseye	1.6.3+dfsg-3	amd64

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Registry entries: Bioconda

plasmidomics

??? missing short description for package plasmidomics :-(

https://www.ira.cinvestav.mx/Investigaci%C3%B3n/Biotecnolog%C3%ADayBioqu%C3%ADmica/ProfesoresInvestigadores/DrRobertWinkler/Software/PlasmidDrawingProgramPlasmidomics02/tabid/778/language/en-US/Default.aspx

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package plasmidomics
Release	Version	Architectures
trixie	0.2.0-10	all
sid	0.2.0-10	all
bullseye	0.2.0-9	all
bookworm	0.2.0-10	all
forky	0.2.0-10	all

Debtags of package plasmidomics:
field	biology, biology:molecular
interface	x11
role	program
scope	utility
uitoolkit	tk
works-with	image:vector
works-with-format	postscript
x11	application

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License: DFSG free

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plasmidseeker

??? missing short description for package plasmidseeker :-(

https://github.com/bioinfo-ut/PlasmidSeeker

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package plasmidseeker
Release	Version	Architectures
forky	1.3+dfsg-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.3+dfsg-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.3+dfsg-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.3+dfsg-1	amd64,arm64,armhf,i386
sid	1.3+dfsg-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

Please cite: Märt Roosaare, Mikk Puustusmaa, Märt Möls, Mihkel Vaher and Maido Remm: PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads. (PubMed,eprint) PeerJ - Life & Environment 6:e4588 (2018)

plast

??? missing short description for package plast :-(

https://plast.inria.fr/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package plast
Release	Version	Architectures
bullseye	2.3.2+dfsg-7	amd64,arm64,armhf,i386
bookworm	2.3.2+dfsg-10	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	2.3.2+dfsg-10	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	2.3.2+dfsg-12	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	2.3.2+dfsg-12	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

Please cite: Van Hoa Nguyen and Dominique Lavenier: PLAST: parallel local alignment search tool for database comparison. (PubMed,eprint) BMC Bioinformatics 10:329 (2009)

Registry entries: Bio.tools

plink

??? missing short description for package plink :-(

http://zzz.bwh.harvard.edu/plink/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package plink
Release	Version	Architectures
forky	1.07+dfsg-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.07+dfsg-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.07+dfsg-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.07+dfsg-3	amd64,arm64,armhf,i386
sid	1.07+dfsg-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

Please cite: Shaun Purcell, Benjamin Neale, Kathe Todd-Brown, Lori Thomas, Manuel A. R. Ferreira, David Bender, Julian Maller, Pamela Sklar, Paul I. W. de Bakker, Mark J. Daly and Pak C. Sham: PLINK: a toolset for whole-genome association and population-based linkage analysis. (PubMed) American Journal of Human Genetics 81(3):559-75 (2007)

Registry entries: Bio.tools SciCrunch Bioconda

plink1.9

??? missing short description for package plink1.9 :-(

https://www.cog-genomics.org/plink/1.9/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package plink1.9
Release	Version	Architectures
sid	1.90~b7.7-241022-2	amd64,arm64,armhf,i386
bookworm	1.90~b6.26-220402-1	amd64,armel,armhf,i386,mipsel
trixie	1.90~b7.7-241022-2	amd64,arm64,armel,armhf,i386
forky	1.90~b7.7-241022-2	amd64,arm64,armhf,i386
bullseye	1.90~b6.21-201019-1	amd64,armhf,i386

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License: DFSG free

Official Debian package

Git

Please cite: Christopher C. Chang, Carson C. Chow, Laurent C.A.M. Tellier, Shashaank Vattikuti, Shaun M. Purcell and James J. Lee: Second-generation PLINK: rising to the challenge of larger and richer datasets. (eprint) GigaScience 4(1):7 (2015)

Registry entries: Bio.tools SciCrunch Bioconda

plink2

??? missing short description for package plink2 :-(

https://www.cog-genomics.org/plink/2.0/

Maintainer: Debian Med Packaging Team (Dylan Aïssi)

Versions of package plink2
Release	Version	Architectures
bullseye	2.00~a3-210203+dfsg-1	amd64,arm64,armhf,i386
trixie	2.00~a6.9-250129+dfsg-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	2.00~a3.5-220809+dfsg-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	2.00~a6.9-250129+dfsg-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	2.00~a6.9-250129+dfsg-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
upstream	260504

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Newer upstream!

License: DFSG free

Official Debian package

Git

Registry entries: SciCrunch

plip

??? missing short description for package plip :-(

https://projects.biotec.tu-dresden.de/plip-web/plip/

Maintainer: Debian Med Packaging Team (Sergio Durigan Junior)

Versions of package plip
Release	Version	Architectures
bullseye	2.1.7+dfsg-1	all
bookworm	2.2.2+dfsg-1	all
forky	2.4.0+dfsg-4	all
trixie	2.4.0+dfsg-4	all
sid	2.4.0+dfsg-4	all
upstream	3.0.0

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License: DFSG free

Official Debian package

Git

Please cite: Sebastian Salentin, Sven Schreiber, V. Joachim Haupt, Melissa F. Adasme and Michael Schroeder: PLIP: fully automated protein–ligand interaction profiler. (eprint) Nucleic Acids Research (W1) (2015)

Registry entries: Bio.tools

poa

??? missing short description for package poa :-(

http://poamsa.sourceforge.net/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package poa
Release	Version	Architectures
sid	2.0+20060928-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	2.0+20060928-10	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	2.0+20060928-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	2.0+20060928-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	2.0+20060928-8	amd64,arm64,armhf,i386

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License: DFSG free

Official Debian package

Git

Please cite: Catherine Grasso and Christopher Lee: Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems. (PubMed) Bioinformatics 20(10):1546-1556 (2004)

Registry entries: Bioconda

populations

??? missing short description for package populations :-(

https://www.bioinformatics.org/~tryphon/populations/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package populations
Release	Version	Architectures
trixie	1.2.33+svn0120106+dfsg-7	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	1.2.33+svn0120106+dfsg-6	amd64,arm64,armhf,i386
sid	1.2.33+svn0120106+dfsg-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.2.33+svn0120106+dfsg-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.2.33+svn0120106+dfsg-6	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

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License: DFSG free

Official Debian package

Git

porechop

??? missing short description for package porechop :-(

https://rrwick.github.io/Porechop

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package porechop
Release	Version	Architectures
bullseye	0.2.4+dfsg-2	amd64,arm64,armhf,i386
bookworm	0.2.4+dfsg-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	0.2.4+dfsg-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	0.2.4+dfsg-6	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
sid	0.2.4+dfsg-9	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

poretools

??? missing short description for package poretools :-(

https://poretools.readthedocs.org

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package poretools
Release	Version	Architectures
bullseye	0.6.0+dfsg-5	all
sid	0.6.0+dfsg-7	all
forky	0.6.0+dfsg-7	all
trixie	0.6.0+dfsg-7	all
bookworm	0.6.0+dfsg-6	all

Popcon: 6 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Nicholas Loman and Aaron Quinlan: Poretools: a toolkit for analyzing nanopore sequence data. (PubMed,eprint) Bioinformatics 30(23):3399-3401 (2014)

Registry entries: Bio.tools Bioconda

pplacer

??? missing short description for package pplacer :-(

https://github.com/matsen/pplacer

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package pplacer
Release	Version	Architectures
sid	1.1~alpha19-8	amd64,arm64,ppc64el,riscv64,s390x
bullseye	1.1~alpha19-4	amd64,arm64
upstream	1.1.alpha22

Popcon: 0 users (0 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: Frederick A Matsen, Robin B Kodner and E Virginia Armbrust: pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. (PubMed,eprint) BMC Bioinformatics 11:538 (2010)

Registry entries: Bioconda

prank

??? missing short description for package prank :-(

https://ariloytynoja.github.io/prank-msa/

Maintainer: Debian Med Packaging Team (Charles Plessy)

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,ppc64el,riscv64,s390x
sid	250331-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	250331-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	0.0.170427+dfsg-3	amd64,arm64,armhf,i386

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License: DFSG free

Official Debian package

Git

Please cite: Ari Löztznoja: Phylogeny-aware alignment with PRANK. (PubMed) Methods Mol. Biol. 1079:155-170 (2014)

Registry entries: Bio.tools Bioconda

predictnls

??? missing short description for package predictnls :-(

https://rostlab.org/services/predictNLS/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package predictnls
Release	Version	Architectures
bullseye	1.0.20-6	all
sid	1.0.20-8	all
forky	1.0.20-8	all
trixie	1.0.20-8	all
bookworm	1.0.20-8	all

Popcon: 5 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Murat Cokol, Rajesh Nair and Burkhard Rost: Finding nuclear localization signals.. (PubMed,eprint) EMBO reports 1(5):411-415 (2000)

Registry entries: Bio.tools SciCrunch

presto

??? missing short description for package presto :-(

https://presto.readthedocs.io

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package presto
Release	Version	Architectures
sid	0.7.6-1	all
bullseye	0.6.2-1	all
bookworm	0.7.1-1	all
trixie	0.7.2-2	all
forky	0.7.6-1	all
upstream	0.7.9

Popcon: 8 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Jason A. Vander Heiden, Gur Yaari, Mohamed Uduman, Joel N.H. Stern, Kevin C. O’Connor, David A. Hafler, Francois Vigneault and Steven H. Kleinstein: pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires. (PubMed,eprint) Bioinformatics 30(13):1930-1932 (2014)

Registry entries: Bio.tools SciCrunch Bioconda

prime-phylo

??? missing short description for package prime-phylo :-(

http://prime.sbc.su.se

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package prime-phylo
Release	Version	Architectures
bookworm	1.0.11-10	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.0.11-14	amd64,arm64,loong64,ppc64el,riscv64,s390x
forky	1.0.11-14	amd64,arm64,ppc64el,riscv64,s390x
bullseye	1.0.11-9	amd64,arm64,armhf,i386
trixie	1.0.11-13	amd64,arm64,ppc64el,riscv64,s390x

Popcon: 8 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Ö. Åkerborg, B. Sennblad, L. Arvestad and J. Lagergren: Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. (PubMed,eprint) Proceedings of the National Academy of Sciences 106(14):5714-5719 (2009)

Registry entries: Bio.tools

primer3

??? missing short description for package primer3 :-(

http://primer3.sourceforge.net

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package primer3
Release	Version	Architectures
sid	2.6.1-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2.4.0-4	amd64,arm64,armhf,i386
bookworm	2.6.1-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	2.6.1-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	2.6.1-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 16 users (37 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Steve Rozen and Helen J. Skaletsky: Primer3 on the WWW for general users and for biologist programmers. (PubMed,eprint) Methods Mol Biol. 132(3):365-86 (2000)

Registry entries: Bio.tools SciCrunch Bioconda

prinseq-lite

??? missing short description for package prinseq-lite :-(

http://prinseq.sourceforge.net/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package prinseq-lite
Release	Version	Architectures
bullseye	0.20.4-6	all
sid	0.20.4-6	all
forky	0.20.4-6	all
trixie	0.20.4-6	all
bookworm	0.20.4-6	all

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License: DFSG free

Official Debian package

Git

Please cite: Schmieder R and Edwards R: Quality control and preprocessing of metagenomic datasets. (PubMed,eprint) Bioinformatics 27(6):863-864 (2011)

proalign

??? missing short description for package proalign :-(

http://loytynojalab.biocenter.helsinki.fi/software/proalign/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package proalign
Release	Version	Architectures
sid	0.603-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	0.603-5	amd64,arm64,armhf,i386
bookworm	0.603-5	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	0.603-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	0.603-6	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

Please cite: Ari Löytynoja and Michel C Milinkovitch: A hidden Markov model for progressive multiple alignment. (PubMed,eprint) Bioinformatics 19(12):1505-13 (2003)

probabel

??? missing short description for package probabel :-(

http://www.genabel.org

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package probabel
Release	Version	Architectures
bullseye	0.5.0+dfsg-4	amd64,arm64,armhf,i386
forky	0.5.0+dfsg-6	amd64
sid	0.5.0+dfsg-6	amd64
bookworm	0.5.0+dfsg-6	amd64,i386
trixie	0.5.0+dfsg-6	amd64

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: probabel-examples

Please cite: Yurii S Aulchenko, Maksim V Struchalin and Cornelia M van Duijn: ProbABEL package for genome-wide association analysis of imputed data.. (PubMed,eprint) BMC Bioinformatics 11:134 (2010)

Registry entries: Bio.tools SciCrunch

probalign

??? missing short description for package probalign :-(

https://web.njit.edu/~usman/probalign/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package probalign
Release	Version	Architectures
bullseye	1.4-9	amd64,arm64,armhf,i386
trixie	1.4-10	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.4-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.4-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.4-10	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

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License: DFSG free

Official Debian package

Git

Please cite: Usman Roshan and Dennis R. Livesay: Probalign: multiple sequence alignment using partition function posterior probabilities. (PubMed,eprint) Bioinformatics 22(22):2715-21 (2006)

Registry entries: SciCrunch

probcons

??? missing short description for package probcons :-(

http://probcons.stanford.edu/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package probcons
Release	Version	Architectures
forky	1.12-15	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.12-13	amd64,arm64,armhf,i386
sid	1.12-15	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.12-14	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.12-14	amd64,arm64,armel,armhf,i386,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

Official Debian package

Git

Please cite: Chuong B. Do, Mahathi S.P. Mahabhashyam, Michael Brudno and Serafim Batzoglou: ProbCons: Probabilistic consistency-based multiple sequence alignment. (PubMed,eprint) Genome Research 15(2):330-340 (2005)

Registry entries: Bio.tools SciCrunch Bioconda

proda

??? missing short description for package proda :-(

http://proda.stanford.edu/

Maintainer: Debian Med Packaging Team (Lance Lin)

Versions of package proda
Release	Version	Architectures
sid	1.0-14	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.0-14	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.0-13	amd64,arm64,armhf,i386
trixie	1.0-14	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.0-13	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,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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Git

Please cite: Tu Minh Phuong, Chuong B. Do, Robert C. Edgar and Serafim Batzoglou: Multiple alignment of protein sequences with repeats and rearrangements. (PubMed,eprint) Nucl. Acids Res. 34(20):5932-5942 (2006)

Registry entries: Bio.tools Bioconda

prodigal

??? missing short description for package prodigal :-(

http://prodigal.ornl.gov/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package prodigal
Release	Version	Architectures
forky	2.6.3-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2.6.3-4	amd64,arm64,armhf,i386
sid	2.6.3-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	2.6.3-6	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	2.6.3-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

Please cite: Doug Hyatt, Gwo-Liang Chen, Philip F. Locascio, Miriam L. Land, Frank W. Larimer and Loren J. Hauser: Prodigal: prokaryotic gene recognition and translation initiation site identification. (PubMed,eprint) BMC Bioinformatics 11:119 (2010)

Registry entries: SciCrunch Bioconda

profbval

??? missing short description for package profbval :-(

https://www.rostlab.org/owiki/index.php/PROFbval

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package profbval
Release	Version	Architectures
bullseye	1.0.22-7	all
trixie	1.0.22-8	all
forky	1.0.22-8	all
bookworm	1.0.22-8	all
sid	1.0.22-8	all

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License: DFSG free

Official Debian package

Git

Please cite: Avner Schlessinger, Guy Yachdav and Burkhard Rost: PROFbval: predict flexible and rigid residues in proteins.. (PubMed) Bioinformatics 22(7):891-3 (2006)

profisis

??? missing short description for package profisis :-(

https://rostlab.org/owiki/index.php/PROFisis

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package profisis
Release	Version	Architectures
forky	1.0.11-7	all
trixie	1.0.11-7	all
bookworm	1.0.11-7	all
bullseye	1.0.11-6	all
sid	1.0.11-7	all

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License: DFSG free

Official Debian package

Git

Please cite: Yanay Ofran and Burkhard Rost: ISIS: interaction sites identified from sequence. (PubMed,eprint) Bioinformatics 23(2):e13-e16 (2007)

Registry entries: Bio.tools

profnet-bval

??? missing short description for package profnet-bval :-(

https://www.predictprotein.org/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package profnet-bval
Release	Version	Architectures
bookworm	1.0.22-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.0.22-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.0.22-8	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	1.0.22-7	amd64,arm64,armhf,i386
forky	1.0.22-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

Please cite: Avner Schlessinger, Guy Yachdav and Burkhard Rost: OPRFbval: predict flexible and rigid residues in proteins. (PubMed,eprint) Bioinformatics 22(7):891-893 (2006 Apr 1)

profnet-chop

??? missing short description for package profnet-chop :-(

https://www.predictprotein.org/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package profnet-chop
Release	Version	Architectures
forky	1.0.22-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.0.22-7	amd64,arm64,armhf,i386
trixie	1.0.22-8	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	1.0.22-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.0.22-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 5 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Avner Schlessinger, Guy Yachdav and Burkhard Rost: OPRFbval: predict flexible and rigid residues in proteins. (PubMed,eprint) Bioinformatics 22(7):891-893 (2006 Apr 1)

profnet-con

??? missing short description for package profnet-con :-(

https://www.predictprotein.org/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package profnet-con
Release	Version	Architectures
trixie	1.0.22-8	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	1.0.22-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.0.22-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.0.22-7	amd64,arm64,armhf,i386
bookworm	1.0.22-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

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Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Avner Schlessinger, Guy Yachdav and Burkhard Rost: OPRFbval: predict flexible and rigid residues in proteins. (PubMed,eprint) Bioinformatics 22(7):891-893 (2006 Apr 1)

profnet-isis

??? missing short description for package profnet-isis :-(

https://www.predictprotein.org/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package profnet-isis
Release	Version	Architectures
trixie	1.0.22-8	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	1.0.22-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.0.22-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.0.22-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.0.22-7	amd64,arm64,armhf,i386

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License: DFSG free

Official Debian package

Git

Please cite: Avner Schlessinger, Guy Yachdav and Burkhard Rost: OPRFbval: predict flexible and rigid residues in proteins. (PubMed,eprint) Bioinformatics 22(7):891-893 (2006 Apr 1)

profnet-md

??? missing short description for package profnet-md :-(

https://www.predictprotein.org/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package profnet-md
Release	Version	Architectures
trixie	1.0.22-8	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	1.0.22-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.0.22-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.0.22-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.0.22-7	amd64,arm64,armhf,i386

Popcon: 5 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Avner Schlessinger, Guy Yachdav and Burkhard Rost: OPRFbval: predict flexible and rigid residues in proteins. (PubMed,eprint) Bioinformatics 22(7):891-893 (2006 Apr 1)

profnet-norsnet

??? missing short description for package profnet-norsnet :-(

https://www.predictprotein.org/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package profnet-norsnet
Release	Version	Architectures
forky	1.0.22-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.0.22-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.0.22-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.0.22-8	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	1.0.22-7	amd64,arm64,armhf,i386

Popcon: 5 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Avner Schlessinger, Guy Yachdav and Burkhard Rost: OPRFbval: predict flexible and rigid residues in proteins. (PubMed,eprint) Bioinformatics 22(7):891-893 (2006 Apr 1)

profnet-prof

??? missing short description for package profnet-prof :-(

https://www.predictprotein.org/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package profnet-prof
Release	Version	Architectures
sid	1.0.22-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.0.22-8	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.0.22-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.0.22-7	amd64,arm64,armhf,i386
bookworm	1.0.22-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 5 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Avner Schlessinger, Guy Yachdav and Burkhard Rost: OPRFbval: predict flexible and rigid residues in proteins. (PubMed,eprint) Bioinformatics 22(7):891-893 (2006 Apr 1)

profnet-snapfun

??? missing short description for package profnet-snapfun :-(

https://www.predictprotein.org/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package profnet-snapfun
Release	Version	Architectures
sid	1.0.22-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.0.22-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	1.0.22-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.0.22-7	amd64,arm64,armhf,i386
trixie	1.0.22-8	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 5 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Avner Schlessinger, Guy Yachdav and Burkhard Rost: OPRFbval: predict flexible and rigid residues in proteins. (PubMed,eprint) Bioinformatics 22(7):891-893 (2006 Apr 1)

profphd-net

??? missing short description for package profphd-net :-(

https://www.predictprotein.org/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package profphd-net
Release	Version	Architectures
bullseye	1.0.22-7	amd64,arm64,armhf,i386
bookworm	1.0.22-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.0.22-8	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.0.22-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.0.22-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 5 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Avner Schlessinger, Guy Yachdav and Burkhard Rost: OPRFbval: predict flexible and rigid residues in proteins. (PubMed,eprint) Bioinformatics 22(7):891-893 (2006 Apr 1)

profphd-utils

??? missing short description for package profphd-utils :-(

https://www.rostlab.org/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package profphd-utils
Release	Version	Architectures
forky	1.0.10-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.0.10-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.0.10-7	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.0.10-6	amd64,arm64,armhf,i386
trixie	1.0.10-7	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 6 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

proftmb

??? missing short description for package proftmb :-(

https://rostlab.org/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package proftmb
Release	Version	Architectures
bullseye	1.1.12-9	amd64,arm64,armhf,i386
sid	1.1.12-11	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.1.12-11	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.1.12-11	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.1.12-11	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 5 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: H. Bigelow and B. Rost: PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins.. (PubMed) Nucleic Acids Res 34(Web Server issue):W186-8 (2006)

Registry entries: Bio.tools

progressivemauve

??? missing short description for package progressivemauve :-(

https://darlinglab.org/mauve/user-guide/mauvealigner.html

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package progressivemauve
Release	Version	Architectures
forky	1.2.0+4713+dfsg-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.2.0+4713+dfsg-5	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.2.0+4713+dfsg-5	amd64,arm64,armhf,i386
sid	1.2.0+4713+dfsg-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.2.0+4713+dfsg-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 10 users (32 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Aaron E. Darling, Bob Mau and Nicole T. Perna: progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement. (PubMed,eprint) PloS one 5(6):e11147 (2010)

Registry entries: Bio.tools SciCrunch

prokka

??? missing short description for package prokka :-(

https://github.com/tseemann/prokka

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package prokka
Release	Version	Architectures
bookworm	1.14.6+dfsg-4	amd64
forky	1.14.6+dfsg-6	all
trixie	1.14.6+dfsg-6	all
bullseye	1.14.6+dfsg-3	amd64
sid	1.14.6+dfsg-6	all
upstream	1.15.6

Popcon: 5 users (32 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: multiqc

Please cite: Torsten Seemann: Prokka: rapid prokaryotic genome annotation. (PubMed,eprint) Bioinformatics 30(14):2068-2069 (2014)

Registry entries: Bio.tools SciCrunch Bioconda

proteinortho

??? missing short description for package proteinortho :-(

https://gitlab.com/paulklemm_PHD/proteinortho

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package proteinortho
Release	Version	Architectures
bookworm	6.1.7+dfsg-1	amd64,arm64,ppc64el,s390x
sid	6.3.1+dfsg-1	amd64,arm64,ppc64el,riscv64,s390x
bullseye	6.0.28+dfsg-1	amd64,arm64
forky	6.3.1+dfsg-1	amd64,arm64,ppc64el,riscv64,s390x
trixie	6.3.1+dfsg-1	amd64,arm64,ppc64el,riscv64,s390x

Popcon: 3 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Marcus Lechner, Sven Findeiß, Lydia Steiner, Manja Marz, Peter F Stadler and Sonja J Prohaska: Proteinortho: Detection of (Co-)orthologs in large-scale analysis. (PubMed,eprint) BMC Bioinformatics 12:124 (2011)

prottest

??? missing short description for package prottest :-(

https://github.com/ddarriba/prottest3

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package prottest
Release	Version	Architectures
bookworm	3.4.2+dfsg-8	all
sid	3.4.2+dfsg-8	all
forky	3.4.2+dfsg-8	all
trixie	3.4.2+dfsg-8	all
bullseye	3.4.2+dfsg-5	all

Popcon: 4 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Diego Darriba, Guillermo L. Taboada, Ramón Doallo and David Posada: ProtTest 3: fast selection of best-fit models of protein evolution. (PubMed,eprint) Bioinformatics 27(8):1164-5 (2011)

Registry entries: Bio.tools SciCrunch

provean

??? missing short description for package provean :-(

http://provean.jcvi.org

Maintainer: Debian Med Packaging Team (Andrius Merkys)

Versions of package provean
Release	Version	Architectures
forky	1.1.5+ds-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.1.5+ds-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.1.5+ds-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.1.5+ds-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 3 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

pscan-chip

??? missing short description for package pscan-chip :-(

http://www.beaconlab.it/pscan_chip_dev/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package pscan-chip
Release	Version	Architectures
trixie	1.1-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	1.1-3	amd64,arm64,armhf,i386
bookworm	1.1-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	1.1-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.1-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 6 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: F. Zambelli, G. Pesole and G. Pavesi: PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments.. (PubMed,eprint) Nucleic Acids Research (2013)

Registry entries: Bio.tools SciCrunch

pscan-tfbs

??? missing short description for package pscan-tfbs :-(

http://www.beaconlab.it/pscan

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package pscan-tfbs
Release	Version	Architectures
bookworm	1.2.2-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.2.2-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.2.2-4	amd64,arm64,armhf,i386
forky	1.2.2-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.2.2-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 72 users (20 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Federico Zambelli, Graziano Pesole and Giulio Pavesi: Pscan: Finding Over-represented Transcription Factor Binding Site Motifs in Sequences from Co-Regulated or Co-Expressed Genes. (PubMed,eprint) Nucleic Acids Research 37(Web Server Issue):W247-W252 (2009)

Registry entries: Bio.tools

psortb

??? missing short description for package psortb :-(

https://www.psort.org/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package psortb
Release	Version	Architectures
sid	3.0.6+dfsg-5	amd64
trixie	3.0.6+dfsg-4	amd64
bookworm	3.0.6+dfsg-3	amd64
bullseye	3.0.6+dfsg-2	amd64

Popcon: 3 users (32 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Nancy Y. Yu, James R. Wagner, Matthew R. Laird, Gabor Melli, Sébastien Rey, Raymond Lo, Phuong Dao, S. Cenk Sahinalp, Martin Ester, Leonard J. Foster and F. S. Brinkman: PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. (PubMed,eprint) Bioinformatics 26(13):1608-1615 (2010)

pullseq

??? missing short description for package pullseq :-(

https://github.com/bcthomas/pullseq

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package pullseq
Release	Version	Architectures
forky	1.0.2-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.0.2-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.0.2-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.0.2-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

pycoqc

??? missing short description for package pycoqc :-(

https://github.com/a-slide/pycoQC

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package pycoqc
Release	Version	Architectures
trixie	2.5.2+dfsg-4	all
sid	2.5.2+dfsg-5	all
bullseye	2.5.2+dfsg-1	all
forky	2.5.2+dfsg-5	all
bookworm	2.5.2+dfsg-3	all

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: multiqc

Registry entries: Bioconda

pycorrfit

??? missing short description for package pycorrfit :-(

https://pycorrfit.readthedocs.io/

Maintainer: Debian Med Packaging Team (Karsten Schöke)

Versions of package pycorrfit
Release	Version	Architectures
bookworm	1.1.7+dfsg-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.1.7+dfsg-1	amd64,arm64,armhf,i386
trixie	1.1.7+nopack-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	1.3.1+nopack-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.3.1+nopack-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Debtags of package pycorrfit:
field	biology, mathematics, physics
interface	x11
role	program
science	modelling, plotting, visualisation
scope	application
uitoolkit	wxwidgets
use	analysing, learning, organizing, viewing
x11	application

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Git

Please cite: Paul Müller, Petra Schwille and Thomas Weidemann: PyCorrFit—generic data evaluation for fluorescence correlation spectroscopy. (PubMed) Bioinformatics 30(17):2532–2533 (2014)

pyensembl

??? missing short description for package pyensembl :-(

https://github.com/openvax/pyensembl

Maintainer: Debian Med Packaging Team (Karsten Schöke)

Versions of package pyensembl
Release	Version	Architectures
forky	2.6.9-1	all
trixie	2.3.13-2	all
bookworm	2.2.4+ds-1	all
sid	2.6.9-1	all
upstream	2.6.13

Popcon: 6 users (36 upd.)^*

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Official Debian package

Git

Registry entries: Bio.tools Bioconda

pyfastx

??? missing short description for package pyfastx :-(

https://github.com/lmdu/pyfastx

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package pyfastx
Release	Version	Architectures
bookworm	0.8.4-2	amd64,arm64,i386,mips64el,ppc64el,s390x
sid	2.3.0-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	2.2.0-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	2.3.0-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

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Git

Please cite: Lianming Du, Qin Liu, Zhenxin Fan, Jie Tang, Xiuyue Zhang, Megan Price, Bisong Yue and Kelei Zhao: Pyfastx: a robust Python package for fast random access to sequences from plain and gzipped FASTA/Q files. (PubMed) Briefings in Bioinformatics 22(4) (2021)

Registry entries: Bioconda

pymol

??? missing short description for package pymol :-(

https://www.pymol.org

Maintainer: Debichem Team (Michael Banck)

Versions of package pymol
Release	Version	Architectures
trixie	3.1.0+dfsg-1	all
bookworm	2.5.0+dfsg-1	all
sid	3.1.0+dfsg-1	all
bullseye	2.4.0+dfsg-2	all
forky	3.1.0+dfsg-1	all

Debtags of package pymol:
field	biology:structural, chemistry
interface	3d, x11
role	program
scope	utility
uitoolkit	tk
use	learning, viewing
works-with	image
x11	application

Popcon: 72 users (51 upd.)^*

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Official Debian package

Git

Registry entries: Bio.tools SciCrunch

Topics:

pyscanfcs

??? missing short description for package pyscanfcs :-(

https://fcs-analysis.github.io/PyScanFCS/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package pyscanfcs
Release	Version	Architectures
sid	0.3.6+ds-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	0.3.6+ds-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	0.3.6+ds-6	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
bullseye	0.3.6+ds-2	amd64,arm64,armhf,i386
bookworm	0.3.6+ds-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

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License: DFSG free

Official Debian package

Git

python3-biomaj3-daemon

??? missing short description for package python3-biomaj3-daemon :-(

https://github.com/genouest/biomaj-daemon

Maintainer: Debian Med Packaging Team (Alexandre Detiste)

Popcon: 8 users (32 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools

python3-bioxtasraw

??? missing short description for package python3-bioxtasraw :-(

https://sourceforge.net/p/bioxtasraw/git/

Maintainer: Debian Science Maintainers (Roland Mas)

Versions of package python3-bioxtasraw
Release	Version	Architectures
bookworm	2.1.1-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el
sid	2.4.1-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	2.3.0-2.1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

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Git

python3-cogent3

??? missing short description for package python3-cogent3 :-(

https://github.com/cogent3/cogent3

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package python3-cogent3
Release	Version	Architectures
bullseye	2020.12.21a+dfsg-4+deb11u1	amd64,arm64,armhf,i386
bookworm	2023.2.12a1+dfsg-2+deb12u1	amd64,arm64,mips64el,ppc64el,s390x
sid	2024.5.7a1+dfsg-3	amd64,arm64
upstream	2026.4.20a0

Popcon: 1 users (0 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

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)

Registry entries: Bio.tools Bioconda

python3-emperor

??? missing short description for package python3-emperor :-(

https://biocore.github.io/emperor/

Maintainer: Debian Med Packaging Team (Alexandre Detiste)

Popcon: 27 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Yoshiki Vázquez-Baeza, Meg Pirrung, Antonio Gonzalez and Rob Knight: EMPeror: a tool for visualizing high-throughput microbial community data. (PubMed) Gigascience 2(1):16 (2013)

Registry entries: Bioconda

python3-geneimpacts

??? missing short description for package python3-geneimpacts :-(

https://github.com/brentp/geneimpacts

Maintainer: Debian Med Packaging Team (Emmanuel Arias)

Versions of package python3-geneimpacts
Release	Version	Architectures
bookworm	0.3.7-4	all
bullseye	0.3.7-3	all
trixie	0.3.7-5	all
forky	0.3.7-5	all
sid	0.3.7-5	all

Popcon: 3 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

python3-gffutils

??? missing short description for package python3-gffutils :-(

https://daler.github.io/gffutils

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package python3-gffutils
Release	Version	Architectures
bullseye	0.10.1-2	all
trixie	0.13-2	all
sid	0.13-5	all
bookworm	0.11.1-3	all
forky	0.13-5	all
upstream	0.14

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Official Debian package

Git

Registry entries: Bio.tools Bioconda

python3-pairtools

??? missing short description for package python3-pairtools :-(

https://github.com/mirnylab/pairtools

Maintainer: Debian Med Packaging Team (Alexandre Detiste)

Versions of package python3-pairtools
Release	Version	Architectures
trixie	1.1.3-1	amd64,arm64,ppc64el,riscv64
sid	1.1.3-2	amd64,arm64,loong64,ppc64el,riscv64
bullseye	0.3.0-2	amd64,arm64,armhf,i386
bookworm	1.0.2-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el
forky	1.1.3-2	amd64,arm64,loong64,ppc64el,riscv64

Popcon: 7 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: python3-pairtools-examples

Registry entries: Bioconda

python3-pybedtools

??? missing short description for package python3-pybedtools :-(

https://daler.github.io/pybedtools/

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package python3-pybedtools
Release	Version	Architectures
forky	0.10.0-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
trixie	0.10.0-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64
bookworm	0.9.0-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el
bullseye	0.8.0-5	amd64,arm64,armhf,i386
sid	0.10.0-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
upstream	0.12.0

Popcon: 24 users (40 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: R. K. Dale, B. S. Pedersen and A. R. Quinlan: Pybedtools: a flexible Python library for manipulating genomic datasets and annotations". Bioinformatics 27(24):3423-3424 (2011)

Registry entries: Bio.tools Bioconda

python3-sqt

??? missing short description for package python3-sqt :-(

https://bitbucket.org/marcelm/sqt

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package python3-sqt
Release	Version	Architectures
sid	0.8.0-9	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
bullseye	0.8.0-4	amd64,arm64,armhf,i386
forky	0.8.0-9	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
trixie	0.8.0-9	amd64,arm64,armel,armhf,i386,ppc64el,riscv64
bookworm	0.8.0-6	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el

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License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

python3-treetime

??? missing short description for package python3-treetime :-(

https://github.com/neherlab/treetime

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package python3-treetime
Release	Version	Architectures
sid	0.11.4-1	all
trixie	0.11.4-1	all
forky	0.11.4-1	all
bullseye	0.8.1-1	all
bookworm	0.9.4-1	all
upstream	0.12.1

Popcon: 12 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

pyvcf

??? missing short description for package pyvcf :-(

https://github.com/jamescasbon/PyVCF

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package pyvcf
Release	Version	Architectures
trixie	0.6.8+git20170215.476169c-11	all
bullseye	0.6.8+git20170215.476169c-7	all
bookworm	0.6.8+git20170215.476169c-9	all
forky	0.6.8+git20170215.476169c-12	all
sid	0.6.8+git20170215.476169c-12	all

Popcon: 7 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

qcat

??? missing short description for package qcat :-(

https://github.com/nanoporetech/qcat

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Popcon: 6 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: qcat-examples

Registry entries: Bioconda

qcumber

??? missing short description for package qcumber :-(

https://gitlab.com/RKIBioinformaticsPipelines/QCumber

Maintainer: Debian Med Packaging Team (Santiago Vila)

Popcon: 7 users (31 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

qiime

??? missing short description for package qiime :-(

https://qiime2.org

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package qiime
Release	Version	Architectures
bookworm	2022.11.1-2	all
sid	2024.5.0-1	all
bullseye	2020.11.1-1	all
upstream	2026.4.0

Popcon: 1 users (0 upd.)^*

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License: DFSG free

Official Debian package

Git

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)

Registry entries: Bio.tools SciCrunch Bioconda

Topics: Microbial ecology

qtltools

??? missing short description for package qtltools :-(

https://qtltools.github.io/qtltools/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package qtltools
Release	Version	Architectures
bullseye	1.3.1+dfsg-2	amd64,arm64,armhf,i386
bookworm	1.3.1+dfsg-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.3.1+dfsg-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.3.1+dfsg-4	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
trixie	1.3.1+dfsg-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 7 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: qtltools-example

Please cite: Olivier Delaneau, Halit Ongen, Andrew A. Brown, Alexandre Fort, Nikolaos I. Panousis and Emmanouil T. Dermitzakis: A complete tool set for molecular QTL discovery and analysis. (eprint) Nature Communications (2017)

Registry entries: Bio.tools

quicktree

??? missing short description for package quicktree :-(

https://github.com/khowe/quicktree/

Maintainer: Debian Med Packaging Team (Lance Lin)

Versions of package quicktree
Release	Version	Architectures
forky	2.5-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	2.5-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	2.5-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	2.5-5	amd64,arm64,armhf,i386
bookworm	2.5-5	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 5 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

quorum

??? missing short description for package quorum :-(

https://github.com/gmarcais/Quorum

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package quorum
Release	Version	Architectures
trixie	1.1.2-2	amd64,arm64,ppc64el,riscv64
bookworm	1.1.1-7	amd64,arm64,mips64el,ppc64el
bullseye	1.1.1-4	amd64,arm64
forky	1.1.2-2	amd64,arm64,loong64,ppc64el,riscv64
sid	1.1.2-2	amd64,arm64,loong64,ppc64el,riscv64

Popcon: 5 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Guillaume Marçais, James A. Yorke and Aleksey Zimin: QuorUM: An Error Corrector for Illumina Reads. (PubMed,eprint) PLoS One 10(6):e0130821 (2015)

Registry entries: SciCrunch

qutemol

??? missing short description for package qutemol :-(

http://qutemol.sourceforge.net/

Maintainer: Debichem Team (Graham Inggs)

Versions of package qutemol
Release	Version	Architectures
sid	0.4.1~cvs20081111-15	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	0.4.1~cvs20081111-13	amd64,arm64,armhf,i386
bookworm	0.4.1~cvs20081111-15	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	0.4.1~cvs20081111-15	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	0.4.1~cvs20081111-15	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x

Popcon: 14 users (36 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Marco Tarini, Paolo Cignoni and Claudio Montani: Ambient Occlusion and Edge Cueing for Enhancing Real Time Molecular Visualization. (eprint) IEEE Transactions on Visualization and Computer Graphics 12(5):1237-1244 (2006)

Registry entries: SciCrunch

r-bioc-annotate

??? missing short description for package r-bioc-annotate :-(

https://bioconductor.org/packages/annotate/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-annotate
Release	Version	Architectures
sid	1.84.0+dfsg-3	all
trixie	1.84.0+dfsg-2	all
bookworm	1.76.0+dfsg-1	all
bullseye	1.68.0+dfsg-1	all
upstream	1.90.0

Popcon: 11 users (35 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

r-bioc-biostrings

??? missing short description for package r-bioc-biostrings :-(

https://bioconductor.org/packages/Biostrings/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-biostrings
Release	Version	Architectures
trixie	2.74.1+dfsg-2	amd64,arm64,ppc64el,riscv64,s390x
bullseye	2.58.0-1	amd64,arm64,armhf,i386
bookworm	2.66.0-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	2.74.1+dfsg-3	amd64,arm64,loong64,ppc64el,riscv64
upstream	2.80.0

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Registry entries: Bio.tools Bioconda

r-bioc-bitseq

??? missing short description for package r-bioc-bitseq :-(

https://bioconductor.org/packages/BitSeq/

Maintainer: Debian R Packages Maintainers (Andreas Tille)

Popcon: 0 users (0 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Peter Glaus, Antti Honkela and Magnus Rattray: Identifying differentially expressed transcripts from RNA-seq data with biological variation. (PubMed,eprint) Bioinformatics 28(13):1721–1728 (2012)

Registry entries: Bio.tools SciCrunch Bioconda

r-bioc-cner

??? missing short description for package r-bioc-cner :-(

https://bioconductor.org/packages/CNEr/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-cner
Release	Version	Architectures
bullseye	1.26.0+dfsg-1	amd64,arm64,armhf,i386
sid	1.42.0+dfsg-4	amd64,arm64,loong64,ppc64el,riscv64
trixie	1.42.0+dfsg-3	amd64,arm64,ppc64el,riscv64,s390x
bookworm	1.34.0+dfsg-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream	1.48.0

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License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools Bioconda

r-bioc-cummerbund

??? missing short description for package r-bioc-cummerbund :-(

https://bioconductor.org/packages/cummeRbund/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Popcon: 4 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: L. Goff and C. Trapnell: cummeRbund: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data (2012)

Registry entries: Bio.tools SciCrunch Bioconda

r-bioc-deseq2

??? missing short description for package r-bioc-deseq2 :-(

https://bioconductor.org/packages/DESeq2/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-deseq2
Release	Version	Architectures
trixie	1.46.0+dfsg-2	amd64,arm64,ppc64el,riscv64,s390x
bullseye	1.30.1+dfsg-1	amd64,arm64,armhf,i386
sid	1.46.0+dfsg-3	amd64,arm64,loong64,ppc64el,riscv64
bookworm	1.38.3+dfsg-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream	1.52.0

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License: DFSG free

Official Debian package

Git

Please cite: Michael I Love, Wolfgang Huber and Simon Anders: Moderated estimation of fold change and dispersion for {RNA}-seq data with {DESeq}2. (eprint) Genome Biol 15(12) (2014)

Registry entries: Bio.tools SciCrunch Bioconda

r-bioc-ebseq

??? missing short description for package r-bioc-ebseq :-(

https://bioconductor.org/packages/EBSeq/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-ebseq
Release	Version	Architectures
trixie	2.4.0-2	amd64,arm64,ppc64el,riscv64,s390x
bookworm	1.38.0-1	all
bullseye	1.30.0-1	all
sid	2.4.0-3	amd64,arm64,loong64,ppc64el,riscv64
upstream	2.10.0

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License: DFSG free

Official Debian package

Git

Please cite: Ning Leng, John A. Dawson, James A. Thomson, Victor Ruotti, Anna I. Rissman, Bart M. G. Smits, Jill D. Haag, Michael N. Gould, Ron M. Stewart and Christina Kendziorski: EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. (eprint) Bioinformatics 29(8):1035-1043 (2013)

Registry entries: Bio.tools SciCrunch Bioconda

r-bioc-edger

??? missing short description for package r-bioc-edger :-(

https://bioconductor.org/packages/edgeR/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-edger
Release	Version	Architectures
bookworm	3.40.2+dfsg-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	4.4.2+dfsg-2	amd64,arm64,loong64,ppc64el,riscv64
bullseye	3.32.1+dfsg-1	amd64,arm64,armhf,i386
trixie	4.4.2+dfsg-1	amd64,arm64,ppc64el,riscv64,s390x
upstream	4.10.0

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License: DFSG free

Official Debian package

Git

Please cite: Mark D. Robinson, Davis J. McCarthy and Gordon K. Smyth: edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. (PubMed,eprint) Bioinformatics 26,:139-140 (2010)

Registry entries: Bio.tools SciCrunch Bioconda

r-bioc-genefilter

??? missing short description for package r-bioc-genefilter :-(

https://bioconductor.org/packages/genefilter/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-genefilter
Release	Version	Architectures
bookworm	1.80.3-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.88.0-3	amd64,arm64,loong64,ppc64el,riscv64
trixie	1.88.0-2	amd64,arm64,ppc64el,riscv64,s390x
bullseye	1.72.1-1	amd64,arm64,armhf,i386
upstream	1.94.0

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License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools Bioconda

r-bioc-geoquery

??? missing short description for package r-bioc-geoquery :-(

https://bioconductor.org/packages/GEOquery/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-geoquery
Release	Version	Architectures
bookworm	2.66.0+dfsg-1	all
trixie	2.74.0+dfsg-2	all
bullseye	2.58.0+dfsg-2	all
sid	2.74.0+dfsg-3	all
upstream	2.80.0

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License: DFSG free

Official Debian package

Git

Please cite: Sean Davis and Paul Meltzer: GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor Bioinformatics 14,:1846-1847, (2007,)

Registry entries: Bio.tools Bioconda

r-bioc-hilbertvis

??? missing short description for package r-bioc-hilbertvis :-(

https://bioconductor.org/packages/HilbertVis

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-hilbertvis
Release	Version	Architectures
bullseye	1.48.0-1	amd64,arm64,armhf,i386
bookworm	1.56.0-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.64.0-2	amd64,arm64,ppc64el,riscv64,s390x
sid	1.64.0-3	amd64,arm64,loong64,ppc64el,riscv64
upstream	1.70.0

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License: DFSG free

Official Debian package

Git

Please cite: Simon Anders: Visualization of genomic data with the Hilbert curve. (PubMed,eprint) Bioinformatics 25(10):1231-1235 (2009)

Registry entries: Bio.tools SciCrunch Bioconda

Remark of Debian Med team: It would be interesting to package HilbertVisGUI as well.

r-bioc-htsfilter

??? missing short description for package r-bioc-htsfilter :-(

https://bioconductor.org/packages/HTSFilter/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-htsfilter
Release	Version	Architectures
bullseye	1.30.1+dfsg-1	all
bookworm	1.38.0+dfsg-2	all
sid	1.46.0+dfsg-3	all
trixie	1.46.0+dfsg-2	all
upstream	1.52.0

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License: DFSG free

Official Debian package

Git

r-bioc-impute

??? missing short description for package r-bioc-impute :-(

https://bioconductor.org/packages/impute/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-impute
Release	Version	Architectures
trixie	1.80.0-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.72.3-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.80.0-3	amd64,arm64,loong64,ppc64el,riscv64
bullseye	1.64.0-1	amd64,arm64,armhf,i386
upstream	1.86.0

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License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools Bioconda

r-bioc-limma

??? missing short description for package r-bioc-limma :-(

https://bioconductor.org/packages/limma/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-limma
Release	Version	Architectures
sid	3.62.2+dfsg-2	amd64,arm64,loong64,ppc64el,riscv64
bookworm	3.54.1+dfsg-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	3.62.2+dfsg-1	amd64,arm64,ppc64el,riscv64,s390x
bullseye	3.46.0+dfsg-1	amd64,arm64,armhf,i386
upstream	3.68.2

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License: DFSG free

Official Debian package

Git

Please cite: Gordon K. Smyth: Limma: linear models for microarray data. (eprint) :397-420 (2005)

Registry entries: Bio.tools SciCrunch Bioconda

r-bioc-megadepth

??? missing short description for package r-bioc-megadepth :-(

https://bioconductor.org/packages/megadepth/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-megadepth
Release	Version	Architectures
sid	1.16.0+ds-3	all
bookworm	1.8.0+ds-1	all
trixie	1.16.0+ds-2	all
upstream	1.22.0

Popcon: 3 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools Bioconda

r-bioc-mergeomics

??? missing short description for package r-bioc-mergeomics :-(

https://bioconductor.org/packages/Mergeomics/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-mergeomics
Release	Version	Architectures
bookworm	1.26.0-1	all
sid	1.34.0-3	all
trixie	1.34.0-2	all
bullseye	1.18.0-1	all
upstream	1.40.0

Popcon: 4 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Le Shu, Yuqi Zhao, Zeyneb Kurt, Sean Geoffrey Byars, Taru Tukiainen, Johannes Kettunen, Luz D. Orozco, Matteo Pellegrini, Aldons J. Lusis, Samuli Ripatti, Bin Zhang, Michael Inouye, Ville-Petteri Mäkinen and Xia Yang: Mergeomics: multidimensional data integration to identify pathogenic perturbations to biological systems. (eprint) BMC Genomics (2016)

Registry entries: Bio.tools

r-bioc-metagenomeseq

??? missing short description for package r-bioc-metagenomeseq :-(

https://bioconductor.org/packages/metagenomeSeq/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-metagenomeseq
Release	Version	Architectures
bullseye	1.32.0-1	all
sid	1.48.1-2	all
bookworm	1.40.0-1	all
trixie	1.48.1-1	all
upstream	1.54.0

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License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools Bioconda

r-bioc-mofa

??? missing short description for package r-bioc-mofa :-(

https://bioconductor.org/packages/MOFA/

Maintainer: Debian R Packages Maintainers (Rebecca N. Palmer)

Versions of package r-bioc-mofa
Release	Version	Architectures
bullseye	1.6.1+dfsg-1	all
bookworm	1.6.1+dfsg-10	all
trixie	1.6.1+dfsg-15	all
sid	1.6.1+dfsg-16	all

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Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Ricard Argelaguet, Britta Velten, Damien Arnol, Sascha Dietrich, Thorsten Zenz, John C Marioni, Florian Buettner, Wolfgang Huber and Oliver Stegle: Link to publication Mol Syst Biol 14:e8124 (2018)

Registry entries: Bioconda

r-bioc-mofa2

??? missing short description for package r-bioc-mofa2 :-(

https://bioconductor.org/packages/MOFA2/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Popcon: users ( upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools Bioconda

r-bioc-multiassayexperiment

??? missing short description for package r-bioc-multiassayexperiment :-(

https://bioconductor.org/packages/MultiAssayExperiment/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-multiassayexperiment
Release	Version	Architectures
trixie	1.32.0+dfsg-2	all
sid	1.32.0+dfsg-3	all
bullseye	1.16.0+dfsg-1	all
bookworm	1.24.0+dfsg-2	all
upstream	1.38.0

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License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools Bioconda

r-bioc-mutationalpatterns

??? missing short description for package r-bioc-mutationalpatterns :-(

https://bioconductor.org/packages/MutationalPatterns/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-mutationalpatterns
Release	Version	Architectures
trixie	3.16.0+dfsg-2	all
sid	3.16.0+dfsg-3	all
bullseye	3.0.1+dfsg-2	all
bookworm	3.8.1+dfsg-1	all
upstream	3.22.0

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License: DFSG free

Official Debian package

Git

r-bioc-phyloseq

??? missing short description for package r-bioc-phyloseq :-(

https://bioconductor.org/packages/phyloseq/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-phyloseq
Release	Version	Architectures
trixie	1.50.0+dfsg-2	all
sid	1.54.0+dfsg-1	all
bookworm	1.42.0+dfsg-1	all
bullseye	1.34.0+dfsg-1	all
upstream	1.56.0

Popcon: 5 users (32 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Paul J. McMurdie and Susan Holmes: phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8(4):e61217 (2013)

Registry entries: Bio.tools SciCrunch Bioconda

r-bioc-rtracklayer

??? missing short description for package r-bioc-rtracklayer :-(

https://bioconductor.org/packages/rtracklayer/

Maintainer: Debian R Packages Maintainers (Rebecca N. Palmer)

Versions of package r-bioc-rtracklayer
Release	Version	Architectures
bullseye	1.50.0-1	amd64,arm64,armhf,i386
trixie	1.66.0-3	amd64,arm64,ppc64el,riscv64,s390x
bookworm	1.58.0-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.66.0-3	amd64,arm64,loong64,ppc64el,riscv64
upstream	1.72.0

Popcon: 36 users (36 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: Michael Lawrence, Robert Gentleman and "Vincent Carey: rtracklayer: an R package for interfacing with genome browsers. (PubMed,eprint) Bioinformatics 25(14):1841-1842 (2009)

Registry entries: Bio.tools Bioconda

r-bioc-scater

??? missing short description for package r-bioc-scater :-(

https://bioconductor.org/packages/scater/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-scater
Release	Version	Architectures
trixie	1.34.1+ds-1	all
sid	1.34.1+ds-2	all
bookworm	1.26.1+ds-1	all
bullseye	1.18.3+ds-4	all
upstream	1.40.0

Popcon: 5 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: McCarthy DJ, Campbell KR, Lun ATL and Willis QF: Scater: pre-processing, quality control, normalisation and visualisation of single-cell RNA-seq data in R. Bioinformatics 33:1179-1186 (2017)

Registry entries: Bio.tools Bioconda

r-bioc-tfbstools

??? missing short description for package r-bioc-tfbstools :-(

https://bioconductor.org/packages/TFBSTools/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-tfbstools
Release	Version	Architectures
bullseye	1.28.0+dfsg-1	amd64,arm64,armhf,i386
trixie	1.44.0+dfsg-2	amd64,arm64,ppc64el,riscv64,s390x
bookworm	1.36.0+dfsg-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.44.0+dfsg-3	amd64,arm64,loong64,ppc64el,riscv64
upstream	1.50.0

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License: DFSG free

Official Debian package

Git

Please cite: Ge Tan and Boris Lenhard: TFBSTools: an R/bioconductor package for transcription factor binding site analysis. (PubMed,eprint) Bioinformatics 32(10):1555–1556 (2016)

Registry entries: Bio.tools Bioconda

r-cran-adegenet

??? missing short description for package r-cran-adegenet :-(

https://cran.r-project.org/package=adegenet

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-adegenet
Release	Version	Architectures
bullseye	2.1.3-1	amd64,arm64,armhf,i386
bookworm	2.1.10-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	2.1.11-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	2.1.11-2	amd64,arm64,loong64,ppc64el,riscv64

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License: DFSG free

Official Debian package

Git

Please cite: Thibaut Jombart: adegenet: a R package for the multivariate analysis of genetic markers. (PubMed,eprint) Bioinformatics 24(11):1403-5 (2008)

Registry entries: SciCrunch

r-cran-adephylo

??? missing short description for package r-cran-adephylo :-(

https://cran.r-project.org/package=adephylo

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-adephylo
Release	Version	Architectures
bullseye	1.1-11-4	amd64,arm64,armhf,i386
bookworm	1.1-13-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.1-17-2	amd64,arm64,loong64,ppc64el,riscv64
trixie	1.1-17-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 7 users (36 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Thibaut Jombart, François Balloux and Stéphane Dray: adephylo: new tools for investigating the phylogenetic signal in biological traits. (PubMed,eprint) Bioinformatics 26(15):1907-1909 (2010)

Registry entries: Bioconda

r-cran-alakazam

??? missing short description for package r-cran-alakazam :-(

https://cran.r-project.org/package=alakazam

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-alakazam
Release	Version	Architectures
bullseye	1.1.0-1	amd64,arm64,armhf,i386
bookworm	1.2.1-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.3.0-1	amd64,arm64,ppc64el,riscv64,s390x
experimental	1.3.0-2~0exp0	amd64,arm64,ppc64el,riscv64,s390x
sid	1.4.3-1	amd64,arm64,loong64,ppc64el,riscv64

Popcon: 6 users (35 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Namita T. Gupta, Jason A. Vander Heiden, Mohamed Uduman, Daniel Gadala-Maria, Gur Yaari and Steven H. Kleinstein: Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data. (eprint) 31(20):3356–3358 (2017)

r-cran-ape

??? missing short description for package r-cran-ape :-(

https://cran.r-project.org/package=ape

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-ape
Release	Version	Architectures
bullseye	5.4-1-1	amd64,arm64,armhf,i386
sid	5.8-1-2	amd64,arm64,loong64,ppc64el,riscv64
sid	5.8-1-1	armhf,i386,s390x
trixie	5.8-1-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	5.7-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 153 users (138 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Emmanuel Paradis and Klaus Schliep: ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics (2018)

r-cran-bio3d

??? missing short description for package r-cran-bio3d :-(

https://cran.r-project.org/package=bio3d

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-bio3d
Release	Version	Architectures
trixie	2.4-5-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	2.4-5-1	armhf,i386,s390x
forky	2.4-5-1	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
sid	2.4-5-2	amd64,arm64,loong64,ppc64el,riscv64
bookworm	2.4-4-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	2.4-1-1	amd64,arm64,armhf,i386

Popcon: 7 users (35 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Barry J. Grant, Ana P. C. Rodrigues, Karim M. ElSawy, J. Andrew McCammon and Leo S. D. Caves: Bio3d: an R package for the comparative analysis of protein structures. (PubMed,eprint) Bioinformatics 22(21):2695-2696 (2006)

r-cran-distory

??? missing short description for package r-cran-distory :-(

https://cran.r-project.org/package=distory

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-distory
Release	Version	Architectures
sid	1.4.5-2	amd64,arm64,loong64,ppc64el,riscv64
sid	1.4.5-1	armhf,i386,s390x
trixie	1.4.5-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	1.4.4-1	amd64,arm64,armhf,i386
bookworm	1.4.4-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 7 users (36 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

r-cran-genabel

??? missing short description for package r-cran-genabel :-(

https://cran.r-project.org/package=GenABEL

Maintainer: Debian R Packages Maintainers (Andreas Tille)

Versions of package r-cran-genabel
Release	Version	Architectures
bookworm	1.8-0-6	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.8-0-4	amd64,arm64,armhf,i386

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License: DFSG free

Official Debian package

Git

Please cite: Yurii S. Aulchenko, Stephan Ripke, Aaron Isaacs and Cornelia M. van Duijn: GenABEL: an R library for genome-wide association analysis. (PubMed,eprint) Bioinformatics 23(10):1294-1296 (2007)

Registry entries: Bio.tools SciCrunch

r-cran-kaos

??? missing short description for package r-cran-kaos :-(

https://cran.r-project.org/package=kaos

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Popcon: 4 users (36 upd.)^*

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License: DFSG free

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Git

Please cite: Hannah F. Löchel, Dominic Eger, Theodor Sperlea and Dominik Heider: Deep learning on chaos game representation for proteins. Bioinformatics (2019)

Registry entries: Bioconda

r-cran-phangorn

??? missing short description for package r-cran-phangorn :-(

https://cran.r-project.org/package=phangorn

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-phangorn
Release	Version	Architectures
trixie	2.12.1+dfsg-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	2.11.1+dfsg-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	2.12.1+dfsg-2	amd64,arm64,loong64,ppc64el,riscv64
bullseye	2.5.5-2	amd64,arm64,armhf,i386
sid	2.12.1+dfsg-1	armhf,i386,s390x

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License: DFSG free

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Git

Please cite: K.P. Schliep: phangorn: phylogenetic analysis in R. (PubMed) Bioinformatics 27(4):592-593 (2011)

r-cran-phytools

??? missing short description for package r-cran-phytools :-(

https://cran.r-project.org/package=phytools

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Popcon: 8 users (36 upd.)^*

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License: DFSG free

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Git

Please cite: Liam J. Revell: phytools: an R package for phylogenetic comparative biology (and other things). (eprint) Methods in Ecology and Evolution 3(2):217-223 (2012)

Registry entries: SciCrunch

r-cran-pscbs

??? missing short description for package r-cran-pscbs :-(

https://cran.r-project.org/package=PSCBS

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Popcon: 4 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Adam B. Olshen, Henrik Bengtsson, Pierre Neuvial, Paul T. Spellman, Richard A. Olshen and Venkatraman E. Seshan: Parent-specific copy number in paired tumor-normal studies using circular binary segmentation. (PubMed,eprint) Bioinformatics 27(15):2038-2046 (2011)

Registry entries: SciCrunch Bioconda

r-cran-qtl

??? missing short description for package r-cran-qtl :-(

https://cran.r-project.org/package=qtl

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-qtl
Release	Version	Architectures
sid	1.74-1	amd64,arm64,loong64,ppc64el,riscv64
trixie	1.70-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	1.70-1	armhf,i386,s390x
bullseye	1.47-9-1	amd64,arm64,armhf,i386
bookworm	1.58-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

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License: DFSG free

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Git

Please cite: Karl W. Broman, Hao Wu, Saunak Sen and Gary A. Churchill: R/qtl: QTL mapping in experimental crosses. (PubMed,eprint) Bioinformatics 19:889-890 (2003)

Registry entries: Bio.tools SciCrunch Bioconda

r-cran-rotl

??? missing short description for package r-cran-rotl :-(

https://cran.r-project.org/package=rotl

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Popcon: 5 users (36 upd.)^*

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License: DFSG free

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Git

r-cran-samr

??? missing short description for package r-cran-samr :-(

https://cran.r-project.org/package=samr

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-samr
Release	Version	Architectures
sid	3.0.1-1	amd64,arm64,loong64,ppc64el,riscv64
trixie	3.0-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	3.0-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	3.0-2	amd64,arm64,armhf,i386

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License: DFSG free

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Git

Registry entries: Bio.tools SciCrunch Bioconda

r-cran-seqinr

??? missing short description for package r-cran-seqinr :-(

https://cran.r-project.org/package=seqinr

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-seqinr
Release	Version	Architectures
bullseye	4.2-5-1	amd64,arm64,armhf,i386
sid	4.2-44-1	amd64,arm64,loong64,ppc64el,riscv64
forky	4.2-44-1	amd64,arm64,loong64,ppc64el,riscv64
trixie	4.2-36-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	4.2-23-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

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License: DFSG free

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Git

Please cite: Delphine Charif and Jean R. Lobry: SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis. :207-232 (2007)

r-cran-seurat

??? missing short description for package r-cran-seurat :-(

https://cran.r-project.org/package=Seurat

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-seurat
Release	Version	Architectures
sid	5.2.1-5	armhf,i386,s390x
bullseye	4.0.0-2	amd64,arm64,armhf,i386
sid	5.5.0-1	amd64,arm64,loong64,ppc64el,riscv64
bookworm	4.3.0-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	5.2.1-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

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License: DFSG free

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Git

Please cite: Rahul Satija, Jeffrey A. Farrell, David Gennert, Alexander F. Schier and Aviv Regev: Spatial reconstruction of single-cell gene expression data. (PubMed) Nature Biotechnology 33:495–502 (2015)

Registry entries: Bioconda

r-cran-shazam

??? missing short description for package r-cran-shazam :-(

https://cran.r-project.org/package=shazam

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Popcon: 4 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

r-cran-spp

??? missing short description for package r-cran-spp :-(

https://cran.r-project.org/package=spp

Maintainer: Debian R Packages Maintainers (Andreas Tille)

Versions of package r-cran-spp
Release	Version	Architectures
trixie	1.16.0-2	amd64,arm64,ppc64el,riscv64,s390x
bookworm	1.16.0-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.16.0-2	amd64,arm64,armhf,i386

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License: DFSG free

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Git

Please cite: Peter V Kharchenko, Michael Y Tolstorukov and Peter J Park: Design and analysis of ChIP-seq experiments for DNA-binding proteins. (PubMed) Nature biotechnology 26(12):1351–1359 (2008)

r-cran-tigger

??? missing short description for package r-cran-tigger :-(

https://cran.r-project.org/package=tigger

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Popcon: 3 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

r-cran-treespace

??? missing short description for package r-cran-treespace :-(

https://cran.r-project.org/package=treespace

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-treespace
Release	Version	Architectures
trixie	1.1.4.3+dfsg-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	1.1.4.4+dfsg-1	amd64,arm64,loong64,ppc64el,riscv64
bullseye	1.1.4.0+dfsg-1	amd64,arm64,armhf,i386
bookworm	1.1.4.1+dfsg-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

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License: DFSG free

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r-cran-tsne

??? missing short description for package r-cran-tsne :-(

https://cran.r-project.org/package=tsne

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-tsne
Release	Version	Architectures
forky	0.2-0-1	all
trixie	0.1-3.1-1	all
bookworm	0.1-3.1-1	all
bullseye	0.1-3-3	all
sid	0.2-0-1	all

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License: DFSG free

Official Debian package

Git

r-cran-vegan

??? missing short description for package r-cran-vegan :-(

https://cran.r-project.org/package=vegan

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-vegan
Release	Version	Architectures
forky	2.6-10+dfsg-3	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
sid	2.6-10+dfsg-3	armhf,i386,s390x
sid	2.6-10+dfsg-4	amd64,arm64,loong64,ppc64el,riscv64
bookworm	2.6-4+dfsg-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	2.5-7+dfsg-1	amd64,arm64,armhf,i386
trixie	2.6-10+dfsg-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
upstream	2.7-3

Popcon: 184 users (137 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Registry entries: SciCrunch

r-cran-webgestaltr

??? missing short description for package r-cran-webgestaltr :-(

https://cran.r-project.org/package=WebGestaltR

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-webgestaltr
Release	Version	Architectures
trixie	0.4.6-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	0.4.6-1	armhf,i386,s390x
bullseye	0.4.4-1	amd64,arm64,armhf,i386
bookworm	0.4.5-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	0.4.6-2	amd64,arm64,loong64,ppc64el,riscv64

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License: DFSG free

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Git

r-cran-wgcna

??? missing short description for package r-cran-wgcna :-(

https://cran.r-project.org/package=WGCNA

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-wgcna
Release	Version	Architectures
bookworm	1.72-1-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.74-1	amd64,arm64,loong64,ppc64el,riscv64
sid	1.73-1	s390x
trixie	1.73-1	amd64,arm64,ppc64el,riscv64,s390x
bullseye	1.69-1	amd64,arm64,armhf,i386

Popcon: 5 users (35 upd.)^*

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License: DFSG free

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Git

Please cite: Peter Langfelder and Steve Horvath: WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9:559 (2012)

Registry entries: Bio.tools Bioconda

r-other-ascat

??? missing short description for package r-other-ascat :-(

https://github.com/Crick-CancerGenomics/ascat

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Popcon: 4 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Peter Van Loo, Silje H Nordgard, Ole Christian Lingjærde, Hege G Russnes, Inga H Rye, Wei Sun, Victor J Weigman, Peter Marynen, Anders Zetterberg, Bjørn Naume, Charles M Perou, Anne-Lise Børresen-Dale and Vessela N Kristensen: Allele-specific Copy Number Analysis of Tumors. (PubMed) PNAS 107(39):16910-5 (2010)

Registry entries: Bio.tools Bioconda

r-other-mott-happy.hbrem

??? missing short description for package r-other-mott-happy.hbrem :-(

http://nebc.nerc.ac.uk/bioinformatics/documentation/happy/happy.txt

Maintainer: Debian R Packages Maintainers (Andreas Tille)

Versions of package r-other-mott-happy.hbrem
Release	Version	Architectures
bullseye	2.4-4	amd64,arm64,armhf,i386
sid	2.4-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	2.4-5	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
trixie	2.4-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	2.4-5	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 4 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Richard Mott, Christopher J. Talbot, Maria G. Turri, Allan C. Collins and Jonathan Flint: A method for fine mapping quantitative trait loci in outbred animal stocks. (PubMed,eprint) Proc. Natl. Acad. Sci. USA 97(23):12649-12654 (2000)

Registry entries: SciCrunch

r-other-rajewsky-dropbead

??? missing short description for package r-other-rajewsky-dropbead :-(

https://github.com/rajewsky-lab/dropbead

Maintainer: Debian R Packages Maintainers (Andreas Tille)

Versions of package r-other-rajewsky-dropbead
Release	Version	Architectures
bullseye	0.3.1+git20180221.d746c6f+ds-3	all
sid	0.3.1+git20180221.d746c6f+ds-3	all
trixie	0.3.1+git20180221.d746c6f+ds-3	all
bookworm	0.3.1+git20180221.d746c6f+ds-3	all

Popcon: 4 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: J. Alles, N. Karaiskos, S. Praktiknjo, S. Grosswendt, P. Wahle, P.-L. Ruffault, S. Ayoub, L. Schreyer, A. Boltengagen, C. Birchmeier, R. Zinzen an, C. Kocks and N. Rajewsky: Cell fixation and preservation for droplet-based single-cell transcriptomics. (PubMed,eprint) BMC Biology 15(44) (2017)

racon

??? missing short description for package racon :-(

https://github.com/lbcb-sci/racon

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package racon
Release	Version	Architectures
sid	1.5.0-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.5.0-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.5.0-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.5.0-3	amd64,arm64,mips64el,ppc64el,s390x
bullseye	1.4.20-1	amd64,arm64,armhf,i386

Popcon: 6 users (36 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Robert Vaser, Ivan Sovic, Niranjan Nagarajan and Mile Sikic: Fast and accurate de novo genome assembly from long uncorrected reads. (PubMed,eprint) Genome Research 27(5):737-746 (2017)

Registry entries: Bioconda

radiant

??? missing short description for package radiant :-(

https://github.com/marbl/Krona

Maintainer: Debian Med Packaging Team (Alexandre Detiste)

Versions of package radiant
Release	Version	Architectures
bookworm	2.8.1+dfsg-2	all
trixie	2.8.1+dfsg-2	all
forky	2.8.1+dfsg-2	all
sid	2.8.1+dfsg-3	all
bullseye	2.7.1+dfsg-4	all

Popcon: 5 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Brian D Ondov, Nicholas H Bergman and Adam M Phillippy: Interactive metagenomic visualization in a Web browser. (PubMed,eprint) BMC Bioinformatics 12:385 (2011)

Registry entries: Bio.tools SciCrunch Bioconda

ragout

??? missing short description for package ragout :-(

https://github.com/fenderglass/Ragout/

Maintainer: Debian Med Packaging Team (Alexandre Detiste)

Versions of package ragout
Release	Version	Architectures
forky	2.3-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	2.3-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	2.3-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	2.3-2	amd64,arm64,armhf,i386
sid	2.3-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 7 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Mikhail Kolmogorov, Joel Armstrong, Brian J. Raney, Ian Streeter, Matthew Dunn, Fengtang Yang, Duncan Odom, Paul Flicek, Thomas M. Keane, David Thybert, Benedict Paten and Son Pham: Chromosome assembly of large and complex genomes using multiple references. (PubMed,eprint) Genome Research 28(11):1720-1732 (2018)

Registry entries: Bioconda

rambo-k

??? missing short description for package rambo-k :-(

http://rambok.sourceforge.net/

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package rambo-k
Release	Version	Architectures
trixie	1.21+dfsg-5	all
forky	1.21+dfsg-6	all
sid	1.21+dfsg-6	all
bullseye	1.21+dfsg-3	all
bookworm	1.21+dfsg-4	all

Popcon: 5 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Simon H. Tausch, Bernhard Y. Renard, Andreas Nitsche and Piotr Wojciech Dabrowski: RAMBO-K: Rapid and Sensitive Removal of Background Sequences from Next Generation Sequencing Data. (PubMed,eprint) PLOS one 10(9):e0137896 (20015)

Registry entries: Bio.tools

rampler

??? missing short description for package rampler :-(

https://github.com/rvaser/rampler

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package rampler
Release	Version	Architectures
forky	2.1.1-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	2.1.1-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2.0.0-1	amd64,arm64,armhf,i386
bookworm	2.1.1-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	2.1.1-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 5 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

rapmap

??? missing short description for package rapmap :-(

https://github.com/COMBINE-lab/RapMap

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package rapmap
Release	Version	Architectures
forky	0.15.0+dfsg-5	amd64
bookworm	0.15.0+dfsg-3	amd64
bullseye	0.15.0+dfsg-1	amd64
sid	0.15.0+dfsg-5	amd64
trixie	0.15.0+dfsg-4	amd64

Popcon: 5 users (38 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Avi Srivastava, Hirak Sarkar, Nitish Gupta and Rob Patro: RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes. (PubMed,eprint) Bioinformatics 32(12):i192-i200 (2016)

Registry entries: Bio.tools Bioconda

rasmol

??? missing short description for package rasmol :-(

http://rasmol.org

Maintainer: Debian Science Maintainers (Marcos Talau)

Versions of package rasmol
Release	Version	Architectures
bullseye	2.7.6.0-2	amd64,arm64,armhf,i386
sid	2.7.6.0-5	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
trixie	2.7.6.0-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	2.7.6.0-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 29 users (42 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: rasmol-doc

Please cite: Roger A. Sayle and E. James Milner-White: RasMol: Biomolecular graphics for all. (PubMed) Trends in Biochemical Sciences (TIBS) 20(9):374 (1995)

Registry entries: Bio.tools

raster3d

??? missing short description for package raster3d :-(

http://www.bmsc.washington.edu/raster3d/raster3d.html

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package raster3d
Release	Version	Architectures
trixie	3.0-7-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	3.0-8-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	3.0-8-3	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
bullseye	3.0-7-2	amd64,arm64,armhf,i386
bookworm	3.0-7-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,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

Popcon: 14 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: E.A. Merritt and D.J. Bacon: Raster3D Photorealistic Molecular Graphics. (PubMed) Methods in Enzymology 277:505-524 (1997)

Registry entries: Bio.tools

rate4site

??? missing short description for package rate4site :-(

https://www.tau.ac.il/~itaymay/cp/rate4site.html

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package rate4site
Release	Version	Architectures
forky	3.0.0-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	3.0.0-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	3.0.0-7	amd64,arm64,armhf,i386
trixie	3.0.0-8	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	3.0.0-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

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Git

Please cite: I. Mayrose, D. Graur, N. Ben-Tal and T. and Pupko: Comparison of site-specific rate-inference methods: Bayesian methods are superior. (PubMed,eprint) Mol Biol Evol 21(2):1781-1791 (2004)

raxml

??? missing short description for package raxml :-(

https://cme.h-its.org/exelixis/web/software/raxml/index.html

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package raxml
Release	Version	Architectures
bullseye	8.2.12+dfsg-6	amd64,arm64,armhf,i386
bookworm	8.2.12+dfsg-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	8.2.13+dfsg-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	8.2.13+dfsg-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	8.2.13+dfsg-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

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Please cite: Alexandros Stamatakis: RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. (PubMed,eprint) Bioinformatics Epub ahead of print (2014)

Registry entries: Bio.tools SciCrunch Bioconda

ray

??? missing short description for package ray :-(

https://denovoassembler.sourceforge.net/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package ray
Release	Version	Architectures
forky	2.3.1-9	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
trixie	2.3.1-9	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	2.3.1-7	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	2.3.1-7	amd64,arm64,armhf,i386
sid	2.3.1-9	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

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Please cite: Sébastien Boisvert, François Laviolette and Jacques Corbeil: Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies. (PubMed,eprint) Journal of Computational Biology 17(11):1519-1533 (2010)

Registry entries: Bio.tools SciCrunch Bioconda

rdp-alignment

??? missing short description for package rdp-alignment :-(

https://github.com/rdpstaff/AlignmentTools

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package rdp-alignment
Release	Version	Architectures
trixie	1.2.0-8	all
bookworm	1.2.0-8	all
forky	1.2.0-8	all
sid	1.2.0-8	all
bullseye	1.2.0-6	all

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License: DFSG free

Official Debian package

Git

Please cite: Jordan A. Fish, Benli Chai, Qiong Wang, Yanni Sun, C. Titus Brown, James M. Tiedje and James R Cole: FunGene: the functional gene pipeline and repository. (PubMed,eprint) Front Microbiology 4:291 (2013)

rdp-classifier

??? missing short description for package rdp-classifier :-(

https://github.com/rdpstaff/classifier

Maintainer: Debian Med Packaging Team (Pierre Gruet)

Popcon: 0 users (0 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Qiong Wang, George M. Garrity, James M. Tiedje and James R. Cole: Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. (PubMed,eprint) Appl Environ Microbiol. 73(16):5261-7 (2007)

rdp-readseq

??? missing short description for package rdp-readseq :-(

https://github.com/rdpstaff/ReadSeq

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package rdp-readseq
Release	Version	Architectures
forky	2.0.2-10	all
sid	2.0.2-10	all
bullseye	2.0.2-7	all
bookworm	2.0.2-9	all
trixie	2.0.2-9	all

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License: DFSG free

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Git

Registry entries: Bioconda

readseq

??? missing short description for package readseq :-(

http://iubio.bio.indiana.edu/soft/molbio/readseq/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package readseq
Release	Version	Architectures
sid	1-16	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1-16	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1-14	amd64,arm64,armhf,i386
bookworm	1-14	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1-15	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Debtags of package readseq:
field	biology, biology:bioinformatics
interface	commandline
role	program
scope	utility
use	converting
works-with-format	plaintext

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License: DFSG free

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Please cite: Don Gilbert: Sequence file format conversion with command-line readseq. (PubMed,eprint) Current Protocols in Bioinformatics Appendix 1:E (2003)

Registry entries: Bio.tools Bioconda

readucks

??? missing short description for package readucks :-(

https://github.com/artic-network/readucks

Maintainer: Debian Med Packaging Team (Andreas Tille)

Popcon: 0 users (0 upd.)^*

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License: DFSG free

Official Debian package

Git

reapr

??? missing short description for package reapr :-(

https://www.sanger.ac.uk/science/tools/reapr

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package reapr
Release	Version	Architectures
sid	1.0.18+dfsg-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.0.18+dfsg-7	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
bullseye	1.0.18+dfsg-5	amd64,arm64,armhf,i386
bookworm	1.0.18+dfsg-5	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el
trixie	1.0.18+dfsg-7	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

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License: DFSG free

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Git

Please cite: Martin Hunt, Taisei Kikuchi, Mandy Sanders, Chris Newbold, Matthew Berriman and Thomas D Otto: REAPR: a universal tool for genome assembly evaluation. (PubMed,eprint) Genome Biology 14(5):R47 (2013)

recan

??? missing short description for package recan :-(

https://github.com/babinyurii/recan

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package recan
Release	Version	Architectures
trixie	0.5+dfsg-1	all
forky	0.5+dfsg-1	all
sid	0.5+dfsg-1	all
bullseye	0.1.2-2	all
bookworm	0.1.5+dfsg-2	all

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License: DFSG free

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relion

??? missing short description for package relion :-(

https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package relion
Release	Version	Architectures
trixie	3.1.3-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	3.1.0-4	amd64,i386
bookworm	3.1.3-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	3.1.3-4	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
upstream	5.1.0

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Git

Please cite: Sjors H. W. Scheres: RELION: implementation of a Bayesian approach to cryo-EM structure determination. (PubMed) J. Struct. Biol. 180(3):519-30 (2012)

relion-gui

??? missing short description for package relion-gui :-(

https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package relion-gui
Release	Version	Architectures
bullseye	3.1.0-4	amd64,i386
sid	3.1.3-4	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
bookworm	3.1.3-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	3.1.3-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
upstream	5.1.0

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Git

Please cite: Sjors H. W. Scheres: RELION: implementation of a Bayesian approach to cryo-EM structure determination. (PubMed) J. Struct. Biol. 180(3):519-30 (2012)

repeatmasker-recon

??? missing short description for package repeatmasker-recon :-(

https://www.repeatmasker.org/

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package repeatmasker-recon
Release	Version	Architectures
trixie	1.08-8	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	1.08-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.08-7	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	1.08-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.08-6	amd64,arm64,armhf,i386

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Git

Please cite: Zhirong Bao and Sean R. Eddy: Automated De Novo Identification of Repeat Sequence Families in Sequenced Genomes. (PubMed,eprint) Genome Research 12(8):1269-76 (2002)

reprof

??? missing short description for package reprof :-(

https://rostlab.org/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

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License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools

resfinder

??? missing short description for package resfinder :-(

https://bitbucket.org/genomicepidemiology/resfinder

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package resfinder
Release	Version	Architectures
bullseye	3.2-3	all
forky	4.4.2-3	all
bookworm	4.3.0-1	all
trixie	4.4.2-2	all
sid	4.4.2-3	all
upstream	4.7.2

Popcon: 5 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Ea Zankari, Henrik Hasman, Salvatore Cosentino, Martin Vestergaard, Simon Rasmussen, Ole Lund, Frank M. Aarestrup and Mette Voldby Larsen: Identification of acquired antimicrobial resistance genes. (PubMed,eprint) Journal of Antimicrobial Chemotherapy 67(11):2640-4 (2012)

rna-star

??? missing short description for package rna-star :-(

https://github.com/alexdobin/STAR/

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package rna-star
Release	Version	Architectures
bookworm	2.7.10b+dfsg-2	amd64,arm64,mips64el,ppc64el
bullseye	2.7.8a+dfsg-2	amd64,arm64
trixie	2.7.11b+dfsg-2	amd64,arm64,ppc64el,riscv64
forky	2.7.11b+dfsg-2	amd64,arm64,loong64,ppc64el,riscv64
sid	2.7.11b+dfsg-2	amd64,arm64,loong64,ppc64el,riscv64

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: multiqc

Please cite: Alexander Dobin, Carrie A. Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson and Thomas R. Gingeras: STAR: ultrafast universal RNA-seq aligner. (PubMed,eprint) Bioinformatics 29(1):15-21 (2012)

Registry entries: Bio.tools SciCrunch Bioconda

Topics: Sequence analysis

rnahybrid

??? missing short description for package rnahybrid :-(

http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/submission.html

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package rnahybrid
Release	Version	Architectures
trixie	2.1.2-8	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
bullseye	2.1.2-6	amd64,arm64,armhf,i386
forky	2.1.2-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	2.1.2-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	2.1.2-7	amd64,arm64,armhf,i386,mips64el,mipsel,ppc64el,s390x

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License: DFSG free

Official Debian package

Git

Please cite: Marc Rehmsmeier, Peter Steffen, Matthias Höchsmann and Robert Giegerich: Fast and effective prediction of microRNA/target duplexes. (PubMed,eprint) RNA 10(10):1507-1517 (2004)

Registry entries: Bio.tools SciCrunch

roary

??? missing short description for package roary :-(

https://sanger-pathogens.github.io/Roary/

Maintainer: Debian Med Packaging Team (Ananthu C V)

Popcon: 7 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane and Julian Parkhill: Roary: Rapid large-scale prokaryote pan genome analysis. (PubMed,eprint) Bioinformatics 31(22):3691-3693 (2015)

Registry entries: Bioconda

rockhopper

??? missing short description for package rockhopper :-(

https://cs.wellesley.edu/~btjaden/Rockhopper/

Maintainer: Debian Med Packaging Team (Pierre Gruet)

Popcon: 5 users (31 upd.)^*

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: multiqc

Please cite: Brian Tjaden: De novo assembly of bacterial transcriptomes from RNA-seq data. (PubMed,eprint) Genome Biology (2015)

roguenarok

??? missing short description for package roguenarok :-(

https://github.com/aberer/RogueNaRok

Maintainer: Debian Med Packaging Team (Adrian Bunk)

Versions of package roguenarok
Release	Version	Architectures
bookworm	1.0.1-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.0.1-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.0.1-3.1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.0.1-3.1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.0-4	amd64,arm64,armhf,i386

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License: DFSG free

Official Debian package

Git

Please cite: Andre J. Aberer, Denis Krompass and Alexandros Stamatakis: Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice. (PubMed,eprint) Systematic Biology 62(1):162-166 (2013)

rsem

??? missing short description for package rsem :-(

https://deweylab.github.io/RSEM/

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package rsem
Release	Version	Architectures
bookworm	1.3.3+dfsg-2	amd64,arm64,mips64el,ppc64el,s390x
sid	1.3.3+dfsg-4	amd64,arm64,loong64,ppc64el,riscv64,s390x
bullseye	1.3.3+dfsg-1	amd64,arm64
forky	1.3.3+dfsg-4	amd64,arm64,ppc64el,riscv64,s390x
trixie	1.3.3+dfsg-3	amd64,arm64,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

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The package is enhanced by the following packages: multiqc

Please cite: Bo Li and Colin Dewey: RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. (PubMed,eprint) BMC Bioinformatics 12(1):323 (2011)

Registry entries: Bio.tools SciCrunch Bioconda

rtax

??? missing short description for package rtax :-(

https://github.com/davidsoergel/rtax/

Maintainer: Debian Med Packaging Team (xiao sheng wen)

Popcon: 5 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: David A. W. Soergel, Neelendu Dey, Rob Knight and Steven E. Brenner: Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. (PubMed,eprint) The ISME Journal 6:1440–1444 (2012)

runcircos-gui

??? missing short description for package runcircos-gui :-(

https://github.com/narunlifescience/runcircos-gui

Maintainer: Debian Med Packaging Team (Steffen Moeller)

Versions of package runcircos-gui
Release	Version	Architectures
sid	0.0+git20200528.82dda8c-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	0.0+git20200528.82dda8c-1	amd64,arm64,armhf,i386
forky	0.0+git20200528.82dda8c-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	0.0+git20200528.82dda8c-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	0.0+git20200528.82dda8c-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

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License: DFSG free

Official Debian package

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saint

??? missing short description for package saint :-(

http://saint-apms.sourceforge.net/Main.html

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package saint
Release	Version	Architectures
trixie	2.5.0+dfsg-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	2.5.0+dfsg-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	2.5.0+dfsg-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2.5.0+dfsg-4	amd64,arm64,armhf,i386
bookworm	2.5.0+dfsg-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 6 users (34 upd.)^*

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License: DFSG free

Official Debian package

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Please cite: A. Breitkreutz, H. Choi, J.R. Sharom, L. Boucher, V. Neduva, B. Larsen, Z.Y. Lin, B.J. Breitkreutz, C. Stark, G. Liu, J. Ahn, D. Dewar-Darch, T. Reguly, X. Tang, R. Almeida, Z.S. Qin, T. Pawson, A.-C. Gingras, A.I. Nesvizhskii and M. Tyers: A global protein kinase and phosphatase interaction network in yeast. (PubMed) Science 328(5981):1043-6 (2010)

Registry entries: Bio.tools

salmid

??? missing short description for package salmid :-(

https://github.com/hcdenbakker/SalmID

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package salmid
Release	Version	Architectures
bookworm	0.1.23-5	all
trixie	0.1.23-5	all
forky	0.1.23-5	all
sid	0.1.23-5	all
bullseye	0.1.23-2	all

Popcon: 28 users (31 upd.)^*

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License: DFSG free

Official Debian package

Git

salmon

??? missing short description for package salmon :-(

https://github.com/COMBINE-lab/salmon

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package salmon
Release	Version	Architectures
sid	1.10.3+ds1-3	amd64,arm64
forky	1.10.3+ds1-3	amd64,arm64
trixie	1.10.2+ds1-1	amd64,arm64
bookworm	1.10.1+ds1-1	amd64,arm64
bullseye	1.4.0+ds1-1	amd64,arm64
upstream	1.11.4

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: multiqc

Please cite: Rob Patro, Geet Duggal, Michael I Love, Rafael A Irizarry and Carl Kingsford: Salmon provides fast and bias-aware quantification of transcript expression. (eprint) Nature Methods 14(4):417-419 (2017)

Registry entries: Bio.tools SciCrunch Bioconda

sambamba

??? missing short description for package sambamba :-(

https://github.com/lomereiter/sambamba

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package sambamba
Release	Version	Architectures
bookworm	1.0+dfsg-1	amd64,arm64
bullseye	0.8.0-1	amd64,arm64
trixie	1.0.1+dfsg-2	amd64,arm64,riscv64
sid	1.0.1+dfsg-3	amd64,arm64,riscv64

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Please cite: Artem Tarasov, Albert J. Vilella, Edwin Cuppen, Isaac J. Nijman and Pjotr Prins: Sambamba: fast processing of NGS alignment formats. (PubMed,eprint) Bioinformatics 31(12):2032-2034 (2015)

Registry entries: Bio.tools Bioconda

samblaster

??? missing short description for package samblaster :-(

https://github.com/GregoryFaust/samblaster

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package samblaster
Release	Version	Architectures
bullseye	0.1.26-1	amd64,arm64,armhf,i386
trixie	0.1.26-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	0.1.26-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	0.1.26-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	0.1.26-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

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The package is enhanced by the following packages: multiqc

Please cite: Gregory G. Faust and Ira M. Hall: SAMBLASTER: fast duplicate marking and structural variant read extraction. (PubMed,eprint) Bioinformatics 30(17):2503-2505 (2014)

Registry entries: Bio.tools SciCrunch Bioconda

samclip

??? missing short description for package samclip :-(

https://github.com/tseemann/samclip

Maintainer: Debian Med Packaging Team (Étienne Mollier)

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License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

samtools

??? missing short description for package samtools :-(

https://www.htslib.org/

Maintainer: Debian Med Packaging Team (Steffen Moeller)

Versions of package samtools
Release	Version	Architectures
sid	1.22.1-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.21-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.16.1-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.11-1	amd64,arm64,armhf,i386
forky	1.22.1-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
upstream	1.23.1

Debtags of package samtools:
field	biology
interface	commandline
network	client
role	program
scope	utility
uitoolkit	ncurses
use	analysing, calculating, filtering
works-with	biological-sequence

Popcon: 58 users (48 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: libbio-samtools-perl multiqc

Please cite: Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin and 1000 Genome Project Data Processing Subgroup: The Sequence Alignment/Map (SAM) Format and SAMtools. (PubMed,eprint) Bioinformatics 25(16):2078-2079 (2009)

Registry entries: Bio.tools SciCrunch Bioconda

savvy-util

??? missing short description for package savvy-util :-(

https://github.com/statgen/savvy

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package savvy-util
Release	Version	Architectures
sid	2.1.0-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	2.1.0-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	2.1.0-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	2.1.0-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
upstream	2.2.0

Popcon: 4 users (34 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

scoary

??? missing short description for package scoary :-(

https://github.com/AdmiralenOla/Scoary

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Popcon: 7 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Ola Brynildsrud, Jon Bohlin, Lonneke Scheffer and Vegard Eldholm: Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary. (PubMed,eprint) Genome Biology 17(238) (2016)

Registry entries: Bio.tools Bioconda

scrappie

??? missing short description for package scrappie :-(

https://github.com/nanoporetech/scrappie

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package scrappie
Release	Version	Architectures
forky	1.4.2-9	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
trixie	1.4.2-8	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
bullseye	1.4.2-7	amd64,arm64,armhf,i386
bookworm	1.4.2-8	amd64,arm64,armhf,i386,mips64el,ppc64el,s390x
sid	1.4.2-9	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 9 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Ryan R. Wick, Louise M. Judd and Kathryn E. Holt: Performance of neural network basecalling tools for Oxford Nanopore sequencing.. (eprint) Genome Biol. 20:129 (2019)

Registry entries: Bioconda

scrm

??? missing short description for package scrm :-(

https://github.com/scrm/scrm

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package scrm
Release	Version	Architectures
sid	1.7.4-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.7.4-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.7.4-1	amd64,arm64,armhf,i386
forky	1.7.4-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.7.4-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 4 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Paul R. Staab, Sha Zhu, Dirk Metzler and Gerton Lunter: scrm: efficiently simulating long sequences using the approximated coalescent with recombination.. (2015)

Registry entries: Bioconda

scythe

??? missing short description for package scythe :-(

https://github.com/vsbuffalo/scythe

Maintainer: Debian Med Packaging Team (Charles Plessy)

Versions of package scythe
Release	Version	Architectures
trixie	0.994+git20141017.20d3cff-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	0.994+git20141017.20d3cff-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	0.994+git20141017.20d3cff-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	0.994+git20141017.20d3cff-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	0.994+git20141017.20d3cff-3	amd64,arm64,armhf,i386

Popcon: 4 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Registry entries: SciCrunch

seaview

??? missing short description for package seaview :-(

https://doua.prabi.fr/software/seaview

Maintainer: Debian Med Packaging Team (Charles Plessy)

Versions of package seaview
Release	Version	Architectures
forky	5.1+20251106-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	5.0.5-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	5.0.5-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	5.1+20251106-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	5.0.4-1	amd64,arm64,armhf,i386

Debtags of package seaview:
field	biology, biology:bioinformatics
interface	x11
network	client
role	program
scope	utility
uitoolkit	fltk
use	comparing, editing, printing, viewing
works-with	biological-sequence
works-with-format	plaintext
x11	application

Popcon: 14 users (37 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: muscle muscle3

Please cite: Manolo Gouy, Stephane Guindon and Olivier Gascuel: SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. (PubMed,eprint) Mol Biol Evol 27(2):221-224 (2010)

Registry entries: Bio.tools SciCrunch

seer

??? missing short description for package seer :-(

https://github.com/johnlees/seer

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package seer
Release	Version	Architectures
sid	1.1.4-9	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.1.4-9	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
trixie	1.1.4-8	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	1.1.4-5	amd64,arm64,armhf,i386
bookworm	1.1.4-7	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 7 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: John A Lees, Minna Vehkala, Niko Välimäki, Simon R Harris, Claire Chewapreecha, Nicholas J Croucher, Pekka Marttinen, Mark R Davies, Andrew C Steer, Stephen Y C Tong, Antti Honkela, Julian Parkhill, Stephen D Bentley and Jukka Corander: Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes. (eprint) bioRxiv (2016)

Registry entries: SciCrunch Bioconda

segemehl

??? missing short description for package segemehl :-(

http://www.bioinf.uni-leipzig.de/Software/segemehl/

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package segemehl
Release	Version	Architectures
sid	0.3.4-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	0.3.4-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	0.3.4-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	0.3.4-5	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	0.3.4-3	amd64,arm64,armhf,i386

Popcon: 4 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Steve Hoffmann, Christian Otto, Stefan Kurtz, Cynthia M. Sharma, Philipp Khaitovich, Jörg Vogel, Peter F. Stadler and Jörg Hackermüller: Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures. (PubMed,eprint) PLoS Computational Biology 5(9):e1000502 (2009)

Registry entries: Bio.tools SciCrunch Bioconda

sepp

??? missing short description for package sepp :-(

https://github.com/smirarab/sepp/

Maintainer: Debian Med Packaging Team (Pierre Gruet)

Popcon: 0 users (0 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

seqan-apps

??? missing short description for package seqan-apps :-(

https://www.seqan.de/

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package seqan-apps
Release	Version	Architectures
experimental	2.5.0~rc3+dfsg-1	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
sid	2.5.2-1	amd64,arm64,loong64,ppc64el,riscv64,s390x
forky	2.5.2-1	amd64,arm64,loong64,ppc64el,riscv64,s390x
trixie	2.4.0+dfsg-16	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	2.4.0+dfsg-15	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	2.4.0+dfsg-14	amd64,arm64,armhf,i386
upstream	2.5.3

Popcon: 6 users (35 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: Andreas Doring, David Weese, Tobias Rausch and Knut Reinert: SeqAn An efficient, generic C++ library for sequence analysis. (PubMed,eprint) BMC Bioinformatics 9(1):11 (2008)

Registry entries: Bio.tools Bioconda

seqan-needle

??? missing short description for package seqan-needle :-(

https://github.com/seqan/needle

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package seqan-needle
Release	Version	Architectures
bookworm	1.0.1.0.0.git.3011926+ds-4	amd64,arm64,mips64el,ppc64el
forky	1.0.3+ds-1	amd64,arm64,loong64,ppc64el,riscv64
trixie	1.0.3+ds-1	amd64,arm64,ppc64el,riscv64
sid	1.0.3+ds-1	amd64,arm64,loong64,ppc64el,riscv64

Popcon: 4 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

seqan-raptor

??? missing short description for package seqan-raptor :-(

https://github.com/seqan/raptor

Maintainer: Debian Med Packaging Team (Marcos Talau)

Versions of package seqan-raptor
Release	Version	Architectures
bookworm	2.0.0.0.git.fecfbca+ds-3	amd64,arm64,mips64el,ppc64el
forky	3.0.1+ds-12	amd64,arm64,loong64,ppc64el,riscv64
sid	3.0.1+ds-12	amd64,arm64,loong64,ppc64el,riscv64
trixie	3.0.1+ds-9	amd64,arm64,ppc64el,riscv64

Popcon: 6 users (37 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Enrico Seiler, Svenja Mehringer, Mitra Darvish, Etienne Turc and Knut Reinert: Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences. iScience 24(7) (2021)

Registry entries: Bio.tools Bioconda

seqkit

??? missing short description for package seqkit :-(

https://github.com/shenwei356/seqkit

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package seqkit
Release	Version	Architectures
bookworm	2.3.1+ds-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	0.15.0+ds-2	amd64,arm64,armhf,i386
trixie	2.9.0+ds-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	2.10.1+ds-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	2.10.1+ds-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
upstream	2.13.0

Popcon: 12 users (41 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: Wei Shen, Shuai Le, Yan Li and Fuquan Hu: SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. (PubMed,eprint) PlosOne 11(10):e0163962 (2016)

Registry entries: Bio.tools Bioconda

seqmagick

??? missing short description for package seqmagick :-(

https://github.com/fhcrc/seqmagick/

Maintainer: Debian Med Packaging Team (Santiago Vila)

Popcon: 6 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

seqprep

??? missing short description for package seqprep :-(

http://seqanswers.com/wiki/SeqPrep

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package seqprep
Release	Version	Architectures
sid	1.3.2-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.3.2-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.3.2-5	amd64,arm64,armhf,i386
trixie	1.3.2-9	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.3.2-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 4 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools SciCrunch Bioconda

seqsero

??? missing short description for package seqsero :-(

https://github.com/denglab/SeqSero

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package seqsero
Release	Version	Architectures
bullseye	1.0.1+dfsg-4	all
forky	1.0.1+dfsg-6	amd64,arm64
bookworm	1.0.1+dfsg-6	amd64,arm64
trixie	1.0.1+dfsg-6	amd64,arm64
sid	1.0.1+dfsg-6	amd64,arm64

Popcon: 5 users (32 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Shaokang Zhang, Yanlong Yin, Marcus B. Jones, Zhenzhen Zhang, Brooke L. Deatherage Kaiser, Blake A. Dinsmore, Collette Fitzgerald, Patricia I. Fields and Xiangyu Deng: Salmonella Serotype Determination Utilizing High-throughput Genome Sequencing Data. (PubMed,eprint) Journal of Clinical Microbiology 53(5):1685-92 (2015)

seqtk

??? missing short description for package seqtk :-(

https://github.com/lh3/seqtk

Maintainer: Debian Med Packaging Team (Lance Lin)

Versions of package seqtk
Release	Version	Architectures
trixie	1.4-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.3-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.3-2	amd64,arm64,armhf,i386
forky	1.4-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.4-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
upstream	1.5

Popcon: 13 users (36 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools Bioconda

sga

??? missing short description for package sga :-(

https://github.com/jts/sga

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package sga
Release	Version	Architectures
bookworm	0.10.15-7	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el
sid	0.10.15-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
forky	0.10.15-7	amd64,arm64,armhf,i386,ppc64el,riscv64
trixie	0.10.15-7	amd64,arm64,armel,armhf,i386,ppc64el,riscv64
bullseye	0.10.15-5	amd64,arm64,armhf,i386

Popcon: 6 users (32 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Jared T. Simpson and Richard Durbin: Efficient de novo assembly of large genomes using compressed data structures.. (PubMed,eprint) Genome Res 22(3):549-555 (2012)

Registry entries: Bio.tools SciCrunch Bioconda

shasta

??? missing short description for package shasta :-(

https://paoloshasta.github.io/shasta/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package shasta
Release	Version	Architectures
trixie	0.12.0-1	amd64,arm64
bookworm	0.11.1-1	amd64,arm64
bullseye	0.7.0-3	amd64,arm64
sid	0.14.0-3	amd64,arm64
forky	0.14.0-3	amd64,arm64

Popcon: 4 users (37 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: K. Shafin, T. Pesout and R. Lorig-Roach et al.: Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nature Biotechnology (2020)

shovill

??? missing short description for package shovill :-(

https://github.com/tseemann/shovill

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package shovill
Release	Version	Architectures
forky	1.1.0-11	amd64
sid	1.1.0-11	amd64
bullseye	1.1.0-4	amd64
bookworm	1.1.0-9	amd64
trixie	1.1.0-9	amd64
upstream	1.4.2

Popcon: 3 users (32 upd.)^*

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License: DFSG free

Official Debian package

Git

sibelia

??? missing short description for package sibelia :-(

https://bioinf.spbau.ru/sibelia

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package sibelia
Release	Version	Architectures
bookworm	3.0.7+dfsg-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	3.0.7+dfsg-3	amd64,arm64,armhf,i386
trixie	3.0.7+dfsg-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	3.0.7+dfsg-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	3.0.7+dfsg-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 6 users (31 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Ilya Minkin, Anand Patel, Mikhail Kolmogorov, Nikolay Vyahhi and Son Pham: Sibelia: A Scalable and Comprehensive Synteny Block Generation Tool for Closely Related Microbial Genomes. Lecture Notes in Computer Science (2013)

Registry entries: Bio.tools Bioconda

sibsim4

??? missing short description for package sibsim4 :-(

http://sibsim4.sourceforge.net/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package sibsim4
Release	Version	Architectures
bullseye	0.20-5	amd64,arm64,armhf,i386
trixie	0.20-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	0.20-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	0.20-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,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

Popcon: 5 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools

sickle

??? missing short description for package sickle :-(

https://github.com/najoshi/sickle

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package sickle
Release	Version	Architectures
trixie	1.33+git20150314.f3d6ae3-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.33+git20150314.f3d6ae3-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.33+git20150314.f3d6ae3-2	amd64,arm64,armhf,i386
sid	1.33+git20150314.f3d6ae3-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.33+git20150314.f3d6ae3-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 4 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: multiqc

Registry entries: Bio.tools SciCrunch Bioconda

sideretro

??? missing short description for package sideretro :-(

https://github.com/galantelab/sideRETRO

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package sideretro
Release	Version	Architectures
trixie	1.1.6-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64
forky	1.1.6-3	amd64,arm64,armhf,i386,ppc64el,riscv64
sid	1.1.6-3	amd64,arm64,armhf,i386,ppc64el,riscv64

Popcon: users ( upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

sigma-align

??? missing short description for package sigma-align :-(

https://www.imsc.res.in/~rsidd/sigma/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package sigma-align
Release	Version	Architectures
bullseye	1.1.3-8	amd64,arm64,armhf,i386
trixie	1.1.3-9	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.1.3-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.1.3-9	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.1.3-9	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Debtags of package sigma-align:
field	biology, biology:bioinformatics
interface	commandline
role	program
scope	utility
use	analysing, comparing
works-with-format	plaintext

Popcon: 5 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Siddharthan, Rahul: Sigma: multiple alignment of weakly-conserved non-coding DNA sequence. (PubMed) BMC Bioinformatics 7(1):143 (2006)

Registry entries: Bio.tools

sim4

??? missing short description for package sim4 :-(

https://globin.bx.psu.edu/html/docs/sim4.html

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package sim4
Release	Version	Architectures
bookworm	0.0.20121010-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	0.0.20121010-9	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	0.0.20121010-9	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	0.0.20121010-8	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	0.0.20121010-8	amd64,arm64,armhf,i386

Debtags of package sim4:
field	biology, biology:bioinformatics
interface	commandline
role	program
scope	utility
use	comparing, searching
works-with-format	plaintext

Popcon: 11 users (36 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Liliana Florea, George Hartzell, Zheng Zhang, Gerald M. Rubin and Webb Miller: A Computer Program for Aligning a cDNA Sequence with a Genomic DNA Sequence. (PubMed,eprint) Genome Research 8:967-974 (1998)

Registry entries: Bio.tools

sim4db

??? missing short description for package sim4db :-(

http://kmer.sourceforge.net

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package sim4db
Release	Version	Architectures
bullseye	0~20150903+r2013-8	amd64,arm64,armhf,i386
sid	0~20150903+r2013-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	0~20150903+r2013-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	0~20150903+r2013-9	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	0~20150903+r2013-10	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x

Popcon: 10 users (38 upd.)^*

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: kmer-examples

Please cite: B. Walenz and L. Florea: Sim4db and leaff: Utilities for fast batched spliced alignment and sequence indexing. (PubMed) Bioinformatics 27(13):1869-1870 (2011)

Registry entries: Bio.tools SciCrunch Bioconda

simka

??? missing short description for package simka :-(

https://github.com/GATB/simka

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package simka
Release	Version	Architectures
trixie	1.5.3-8	amd64,arm64,ppc64el,riscv64
bullseye	1.5.3-4	amd64,arm64,i386
bookworm	1.5.3-7	amd64,arm64,mips64el,ppc64el
sid	1.5.3-10	amd64,arm64,loong64,ppc64el,riscv64
forky	1.5.3-10	amd64,arm64,ppc64el,riscv64

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License: DFSG free

Official Debian package

Git

Please cite: Gaëtan Benoit, Pierre Peterlongo, Mahendra Mariadassou, Erwan Drezen, Sophie Schbath, Domonique Lavenier and Claire Lemaitre: Multiple comparative metagenomics using multiset k-mer counting. :25 (2016)

Registry entries: Bioconda

simkamin

??? missing short description for package simkamin :-(

https://github.com/GATB/simka

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package simkamin
Release	Version	Architectures
forky	1.5.3-10	all
trixie	1.5.3-8	all
bookworm	1.5.3-7	all
bullseye	1.5.3-4	all
sid	1.5.3-10	all

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License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

ska

??? missing short description for package ska :-(

https://github.com/simonrharris/SKA

Maintainer: Debian Med Packaging Team (Steve M. Robbins)

Versions of package ska
Release	Version	Architectures
forky	1.0+dfsg-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.0+dfsg-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.0+dfsg-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.0+dfsg-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

Please cite: S. R. Harris: SKA: Split Kmer Analysis Toolkit for Bacterial Genomic Epidemiology. (eprint) bioRxiv (2018)

Registry entries: Bioconda

skesa

??? missing short description for package skesa :-(

https://github.com/ncbi/SKESA

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package skesa
Release	Version	Architectures
trixie	2.4.0-6	amd64,arm64
forky	2.4.0-8	amd64,arm64
bullseye	2.4.0-1	amd64,i386
sid	2.4.0-8	amd64,arm64
bookworm	2.4.0-6	amd64,arm64

Popcon: 5 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Alexandre Souvorov, Richa Agarwala and David J. Lipman: SKESA: strategic k-mer extension for scrupulous assemblies. (PubMed,eprint) Genome Biology 19(1):153 (2018)

Registry entries: Bioconda

skewer

??? missing short description for package skewer :-(

https://github.com/relipmoc/skewer

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package skewer
Release	Version	Architectures
bullseye	0.2.2-2	amd64,arm64,armhf,i386
bookworm	0.2.2-6	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	0.2.2-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	0.2.2-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	0.2.2-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: multiqc

Please cite: H. Jiang, R. Lei, S. W. Ding and S. Zhu: Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.. (eprint) BMC Bioinformatics 15:182 (2014)

Registry entries: Bio.tools Bioconda

smalt

??? missing short description for package smalt :-(

https://www.sanger.ac.uk/science/tools/smalt-0

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package smalt
Release	Version	Architectures
forky	0.7.6-13	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	0.7.6-12	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	0.7.6-9	amd64,arm64,armhf,i386
trixie	0.7.6-13	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	0.7.6-13	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools SciCrunch Bioconda

Remark of Debian Med team: This can be regarded as successor of ssaha2

This program is from the same author as ssaha2 and according to its author faster and more precise than ssaha2 (except for sequences > 2000bp).

smithwaterman

??? missing short description for package smithwaterman :-(

https://github.com/ekg/smithwaterman

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package smithwaterman
Release	Version	Architectures
trixie	0.0+git20160702.2610e25-12	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	0.0+git20160702.2610e25-12	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	0.0+git20160702.2610e25-11	amd64,arm64,armhf,i386
bookworm	0.0+git20160702.2610e25-12	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	0.0+git20160702.2610e25-12	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

smrtanalysis

??? missing short description for package smrtanalysis :-(

https://www.pacb.com/products-and-services/analytical-software/smrt-analysis/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Popcon: 0 users (0 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools SciCrunch

snap

??? missing short description for package snap :-(

https://github.com/KorfLab/SNAP

Maintainer: Debian Med Packaging Team (Pierre Gruet)

Versions of package snap
Release	Version	Architectures
forky	2013-11-29-11	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2013-11-29-11	amd64,arm64,armhf,i386
trixie	2013-11-29-11	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	2013-11-29-11	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	2013-11-29-11	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

Please cite: Ian Korf: Gene finding in novel Genomes. (PubMed,eprint) BMC Bioinformatics 5:59 (2004)

Registry entries: Bio.tools

snap-aligner

??? missing short description for package snap-aligner :-(

https://snap.cs.berkeley.edu/

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package snap-aligner
Release	Version	Architectures
bullseye	1.0.0+dfsg-2	amd64,arm64
bookworm	2.0.2+dfsg-1	amd64,arm64,mips64el,ppc64el
trixie	2.0.3+dfsg-2	amd64,arm64,ppc64el,riscv64
forky	2.0.5+dfsg-1	amd64,arm64,loong64,ppc64el,riscv64
sid	2.0.5+dfsg-1	amd64,arm64,loong64,ppc64el,riscv64

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License: DFSG free

Official Debian package

Git

Please cite: Matei Zaharia, William J. Bolosky, Kristal Curtis, Armando Fox, David Patterson, Scott Shenker, Ion Stoica, Richard M. Karp and Taylor Sittler: Faster and More Accurate Sequence Alignment with SNAP. (eprint) arXiv preprint arXiv:1111.5572 (2011)

Registry entries: SciCrunch

sniffles

??? missing short description for package sniffles :-(

https://github.com/fritzsedlazeck/Sniffles

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package sniffles
Release	Version	Architectures
forky	2.6.0-1	all
bookworm	2.0.7-1	all
bullseye	1.0.12b+ds-1	amd64,arm64,armhf,i386
trixie	2.6.0-1	all
sid	2.6.0-1	all
upstream	2.8.0

Popcon: 5 users (34 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: Fritz J. Sedlazeck, Philipp Rescheneder, Moritz Smolka, Han Fang, Maria Nattestad, Arndt von Haeseler and Michael Schatz: Accurate detection of complex structural variations using single molecule sequencing. (eprint) bioRxiv (2017)

Registry entries: Bio.tools Bioconda

snippy

??? missing short description for package snippy :-(

https://github.com/tseemann/snippy/

Maintainer: Debian Med Packaging Team (Santiago Vila)

Popcon: 4 users (32 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

snp-sites

??? missing short description for package snp-sites :-(

https://github.com/sanger-pathogens/snp-sites

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package snp-sites
Release	Version	Architectures
forky	2.5.1-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	2.5.1-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	2.5.1-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	2.5.1-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	2.5.1-1	amd64,arm64,armhf,i386

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License: DFSG free

Official Debian package

Git

Please cite: Andrew J. Page, Ben Taylor, Aidan J. Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane and Simon R. Harris: SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. (eprint) Microbial Genomics 2(4) (2016)

Topics: Genetic variation

snpeff

??? missing short description for package snpeff :-(

https://pcingola.github.io/SnpEff/

Maintainer: Debian Med Packaging Team (Alexandre Detiste)

Versions of package snpeff
Release	Version	Architectures
forky	5.4.b+dfsg-2	all
trixie	5.2.f+dfsg-1	all
sid	5.4.b+dfsg-2	all
bookworm	5.1+d+dfsg-3	all
upstream	5.4c

Popcon: 6 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: multiqc

Please cite: Pablo Cingolani, Adrian Platts, Le Lily Wang, Melissa Coon, Tung Nguyen, Luan Wang, Susan J. Land, Douglas M. Ruden and Xiangyi Lu: A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w^1118; iso-2; iso-3. (PubMed,eprint) Fly 6(2):80-92 (2012)

Registry entries: Bio.tools SciCrunch Bioconda

snpomatic

??? missing short description for package snpomatic :-(

https://github.com/magnusmanske/snpomatic

Maintainer: Debian Med Packaging Team (Sascha Steinbiss)

Versions of package snpomatic
Release	Version	Architectures
sid	1.0-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.0-7	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.0-6	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.0-5	amd64,arm64,armhf,i386
forky	1.0-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

Please cite: Heinrich Magnus Manske and Dominic P. Kwiatkowski: SNP-o-matic. (PubMed,eprint) Bioinformatics 25(18):2434-2435 (2009)

Registry entries: Bio.tools Bioconda

Topics: Genetic variation; Mapping

snpsift

??? missing short description for package snpsift :-(

https://pcingola.github.io/SnpEff/ss_introduction/

Maintainer: Debian Med Packaging Team (Pierre Gruet)

Popcon: 5 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

soapaligner

??? missing short description for package soapaligner :-(

https://web.archive.org/web/20190127081222/http://soap.genomics.org.cn/soapaligner.html

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package soapaligner
Release	Version	Architectures
bookworm	2.20-5	amd64
sid	2.20-6	amd64
trixie	2.20-5	amd64
forky	2.20-6	amd64
bullseye	2.20-5	amd64

Popcon: 4 users (32 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Ruiqiang Li, Yingrui Li, Karsten Kristiansen and Jun Wang: SOAP: short oligonucleotide alignment program. (PubMed,eprint) Genome Res. 24(5):713-714 (2008)

Registry entries: Bio.tools SciCrunch Bioconda

soapdenovo

??? missing short description for package soapdenovo :-(

http://soap.genomics.org.cn/soapdenovo.html

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package soapdenovo
Release	Version	Architectures
bookworm	1.05-6	amd64
trixie	1.05-6	amd64
sid	1.05-7	amd64
forky	1.05-7	amd64
bullseye	1.05-6	amd64

Popcon: 7 users (31 upd.)^*

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License: DFSG free

Official Debian package

Git

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)

Registry entries: Bio.tools SciCrunch

soapdenovo2

??? missing short description for package soapdenovo2 :-(

http://soap.genomics.org.cn/soapdenovo.html

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package soapdenovo2
Release	Version	Architectures
trixie	242+dfsg-4	amd64
bullseye	242+dfsg-1	amd64
bookworm	242+dfsg-3	amd64
forky	242+dfsg-5	amd64
sid	242+dfsg-5	amd64

Popcon: 6 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

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)

Registry entries: Bio.tools SciCrunch Bioconda

soapsnp

??? missing short description for package soapsnp :-(

http://soap.genomics.org.cn/soapsnp.html

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package soapsnp
Release	Version	Architectures
bullseye	1.03-4	amd64,arm64,armhf,i386
sid	1.03-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.03-5	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.03-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.03-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 5 users (32 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K and Wang J.: SNP detection for massively parallel whole-genome resequencing. (PubMed,eprint) Genome Res. 19(6):1124-1132 (2009)

Registry entries: Bio.tools SciCrunch

sortmerna

??? missing short description for package sortmerna :-(

https://github.com/sortmerna/sortmerna

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package sortmerna
Release	Version	Architectures
forky	4.3.7-3	amd64,i386
bullseye	2.1-5	amd64,i386
sid	4.3.7-3	amd64,i386
bookworm	4.3.6-2	amd64,i386
trixie	4.3.7-2	amd64,i386
upstream	5.0.0

Popcon: 5 users (34 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: multiqc

Please cite: Evguenia Kopylova, Laurent Noé and Hélène Touzet: SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data". (PubMed,eprint) Bioinformatics 28(24):3211-3217 (2012)

Registry entries: Bio.tools SciCrunch Bioconda

sourmash

??? missing short description for package sourmash :-(

https://github.com/sourmash-bio/sourmash

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Popcon: 6 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: C. Titus Brown and Luiz Irber: sourmash: a library for MinHash sketching of DNA. (eprint) The Journal of Open Source Software 1(5):27 (2016)

Registry entries: Bio.tools Bioconda

spaced

??? missing short description for package spaced :-(

https://spaced.gobics.de/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package spaced
Release	Version	Architectures
bullseye	1.2.0-201605+dfsg-2	amd64,arm64,armhf,i386
bookworm	1.2.0-201605+dfsg-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.2.0-201605+dfsg-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.2.0-201605+dfsg-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.2.0-201605+dfsg-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 5 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Burkhard Morgenstern, Bingyao Zhu, Sebastian Horwege and Chris-Andre Leimeister: Estimating evolutionary distances between genomic sequences from spaced-words matches. (PubMed,eprint) Algorithms for Molecular Biology 10(1):1-12 (2015)

spades

??? missing short description for package spades :-(

https://github.com/ablab/spades

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package spades
Release	Version	Architectures
trixie	4.0.0+really3.15.5+dfsg-1	amd64
bullseye	3.13.1+dfsg-2	amd64
sid	4.0.0+really3.15.5+dfsg-3	amd64
forky	4.0.0+really3.15.5+dfsg-3	amd64
bookworm	3.15.5+dfsg-2	amd64
upstream	4.2.0

Popcon: 4 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A. Gurevich, Mikhail Dvorkin, Alexander S. Kulikov, Valery M. Lesin, Sergey I. Nikolenko, Son Pham, Andrey D. Prjibelski, Alexey V. Pyshkin, Alexander V. Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max A. Alekseyev and Pavel A. Pevzner: SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. (PubMed,eprint) Journal of Computational Biology 19(5):455-477 (2012)

Registry entries: Bio.tools SciCrunch Bioconda

spaln

??? missing short description for package spaln :-(

https://github.com/ogotoh/spaln

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package spaln
Release	Version	Architectures
bullseye	2.4.1+dfsg-3	amd64,arm64,armhf,i386
bookworm	2.4.13f+dfsg-1	amd64,arm64,mips64el,ppc64el,s390x
sid	3.0.7+dfsg-1	amd64,arm64,loong64,ppc64el,riscv64,s390x
forky	3.0.7+dfsg-1	amd64,arm64,loong64,ppc64el,riscv64,s390x
trixie	3.0.2+dfsg-2	amd64,arm64,ppc64el,riscv64,s390x

Popcon: 7 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Osamu Gotoh: A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence. (PubMed) Nucleic Acids Res. 36(8):2630-8 (2008)

Registry entries: Bioconda

spoa

??? missing short description for package spoa :-(

https://github.com/rvaser/spoa

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package spoa
Release	Version	Architectures
forky	4.1.5-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	4.0.7+ds-1	amd64,arm64,armhf,i386
bookworm	4.0.8-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	4.1.5-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	4.1.4-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 5 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

sprai

??? missing short description for package sprai :-(

https://web.archive.org/web/20180316202959/http://zombie.cb.k.u-tokyo.ac.jp/sprai/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package sprai
Release	Version	Architectures
forky	0.9.9.23+dfsg1-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	0.9.9.23+dfsg1-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	0.9.9.23+dfsg1-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	0.9.9.23+dfsg1-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	0.9.9.23+dfsg1-2	amd64,arm64,armhf,i386

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License: DFSG free

Official Debian package

Git

spread-phy

??? missing short description for package spread-phy :-(

https://www.kuleuven.be/aidslab/phylogeography/SPREAD.html

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package spread-phy
Release	Version	Architectures
forky	1.0.7+dfsg-5	all
bullseye	1.0.7+dfsg-3	all
bookworm	1.0.7+dfsg-5	all
trixie	1.0.7+dfsg-5	all
sid	1.0.7+dfsg-5	all

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Official Debian package

Git

Please cite: Filip Bielejec, Andrew Rambaut, Marc A. Suchard and Philippe Lemey: SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics. (PubMed,eprint) Bioinformatics 27(20):2910-2912 (2011)

sra-toolkit

??? missing short description for package sra-toolkit :-(

https://github.com/ncbi/sra-tools/

Maintainer: Debian Med Packaging Team (Aaron M. Ucko)

Versions of package sra-toolkit
Release	Version	Architectures
sid	3.2.1+dfsg-6	amd64,arm64
bullseye	2.10.9+dfsg-2	amd64
forky	3.2.1+dfsg-6	amd64,arm64
trixie	3.2.1+dfsg-4	amd64,arm64
bookworm	3.0.3+dfsg-6~deb12u1	amd64,arm64
upstream	4760-2.9.7

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License: DFSG free

Official Debian package

Git

srst2

??? missing short description for package srst2 :-(

https://katholt.github.io/srst2/

Maintainer: Debian Med Packaging Team (Alexandre Detiste)

Versions of package srst2
Release	Version	Architectures
bookworm	0.2.0-9	amd64,arm64,mips64el,ppc64el
sid	0.2.0-14	amd64,arm64,loong64,ppc64el,riscv64
trixie	0.2.0-13	amd64,arm64,ppc64el,riscv64
forky	0.2.0-14	amd64,arm64,loong64,ppc64el,riscv64
bullseye	0.2.0-8	amd64,arm64

Popcon: 4 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Michael Inouye, Harriet Dashnow, Lesley-Ann Raven, Mark B Schultz, Bernard J Pope, Takehiro Tomita, Justin Zobel and Kathryn E Holt: SRST2: Rapid genomic surveillance for public health and hospital microbiology labs. (PubMed,eprint) Genome Medicine 6(11):90 (2014)

Registry entries: Bioconda

ssake

??? missing short description for package ssake :-(

https://www.bcgsc.ca/platform/bioinfo/software/ssake

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Popcon: 6 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Rene L. Warren, Granger G. Sutton, Steven J. M. Jones and Robert A. Holt: Assembling millions of short DNA sequences using SSAKE. (PubMed,eprint) Bioinformatics 23(4):500-501 (2007)

Registry entries: Bio.tools SciCrunch Bioconda

Topics: Sequence assembly

sspace

??? missing short description for package sspace :-(

https://github.com/nsoranzo/sspace_basic

Maintainer: Debian Med Packaging Team (Sascha Steinbiss)

Versions of package sspace
Release	Version	Architectures
forky	2.1.1+dfsg-7	all
sid	2.1.1+dfsg-7	all
bookworm	2.1.1+dfsg-7	all
bullseye	2.1.1+dfsg-5	all
trixie	2.1.1+dfsg-7	all

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License: DFSG free

Official Debian package

Git

Please cite: Marten Boetzer, Christiaan V. Henkel, Hans J. Jansen, Derek Butler and Walter Pirovano: Scaffolding pre-assembled contigs using SSPACE. (PubMed,eprint) Bioinformatics 27(4):578-579 (2010)

Registry entries: Bio.tools SciCrunch Bioconda

ssw-align

??? missing short description for package ssw-align :-(

https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package ssw-align
Release	Version	Architectures
experimental	1.2.5-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.1-16	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.1-16	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.1-15	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.1-13	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.1-13	amd64,arm64,armhf,i386
upstream	1.2.5

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License: DFSG free

Official Debian package

Git

stacks

??? missing short description for package stacks :-(

https://creskolab.uoregon.edu/stacks/

Maintainer: Debian Med Packaging Team (Marcos Talau)

Versions of package stacks
Release	Version	Architectures
sid	2.68+dfsg-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	2.62+dfsg-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	2.68+dfsg-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	2.68+dfsg-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2.55+dfsg-1	amd64,arm64,armhf,i386

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: multiqc

Please cite: Julian Catchen, Paul A. Hohenlohe, Susan Bassham, Angel Amores and William A. Cresko: Stacks: an analysis tool set for population genomics. (PubMed) Molecular Ecology 22(11):3124-40 (2013)

Registry entries: Bio.tools SciCrunch Bioconda

staden

??? missing short description for package staden :-(

https://sourceforge.net/projects/staden/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package staden
Release	Version	Architectures
bookworm	2.0.0+b11-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	2.0.0+b11-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	2.0.0+b11-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	2.0.0+b11-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2.0.0+b11-4	amd64,arm64,armhf,i386

Popcon: 7 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: James K. Bonfield and Andrew Whitwham: Gap5--editing the billion fragment sequence assembly. (PubMed,eprint) Bioinformatics 26(14):1699-1703 (2010)

Registry entries: Bio.tools SciCrunch

staden-io-lib-utils

??? missing short description for package staden-io-lib-utils :-(

https://github.com/jkbonfield/io_lib

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package staden-io-lib-utils
Release	Version	Architectures
trixie	1.15.0-1.1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	1.15.1-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.15.1-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.14.13-4	amd64,arm64,armhf,i386
bookworm	1.14.15-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream	1-16-0

Debtags of package staden-io-lib-utils:
biology	nuceleic-acids, peptidic
field	biology, biology:bioinformatics
interface	commandline
role	program
scope	utility
use	analysing

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Newer upstream!

License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

stringtie

??? missing short description for package stringtie :-(

https://ccb.jhu.edu/software/stringtie/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package stringtie
Release	Version	Architectures
trixie	2.2.1+ds-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	2.2.1+ds-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	3.0.3+ds-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2.1.4+ds-4	amd64,arm64,armhf,i386
sid	3.0.3+ds-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 4 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Mihaela Pertea, Geo M. Pertea, Corina .M. Antonescu, Tsung-Cheng Chang, Joshua T. Mendell and Steven L. Salzberg: StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology 33:290–295 (2015)

Registry entries: Bio.tools SciCrunch Bioconda

subread

??? missing short description for package subread :-(

http://sourceforge.net/projects/subread/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package subread
Release	Version	Architectures
forky	2.0.8+dfsg-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
bullseye	2.0.1+dfsg-1	amd64,arm64,armhf,i386
bookworm	2.0.3+dfsg-1	amd64,arm64,armel,armhf,i386,ppc64el
trixie	2.0.8+dfsg-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64
sid	2.0.8+dfsg-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
upstream	2.1.1

Popcon: 12 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Yang Lian, Gordon K. Smyth and Wei Shi: The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads. (PubMed) Nucleic Acids Research 47(8):e47-e47 (2019)

Registry entries: Bio.tools SciCrunch Bioconda

suitename

??? missing short description for package suitename :-(

http://kinemage.biochem.duke.edu/software/suitename.php

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package suitename
Release	Version	Architectures
bullseye	0.3.070919+git20180613.ebb1325-2	amd64,arm64,armhf,i386
bookworm	0.4.130509+git20210223.ebb1325-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	0.4.130509+git20210223.ebb1325-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	0.4.130509+git20210223.ebb1325-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	0.4.130509+git20210223.ebb1325-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 4 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Jane S. Richardson, Bohdan Schneider, Laura W. Murray, Gary J. Kapral, Robert M. Immormino, Jeffrey J. Headd, David C. Richardson, Daniela Ham, Eli Hershkovits, Loren Dean Williams, Kevin S. Keating, Anna Marie Pyle, David Micallef, John Westbrook and Helen M. Berman: RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). (PubMed,eprint) RNA 14(3):465-481 (2008)

sumaclust

??? missing short description for package sumaclust :-(

http://metabarcoding.org/sumaclust

Maintainer: Debian Med Packaging Team (Pierre Gruet)

Versions of package sumaclust
Release	Version	Architectures
sid	1.0.36+ds-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.0.36+ds-1	amd64,arm64,armhf,i386
trixie	1.0.36+ds-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.0.36+ds-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	1.0.36+ds-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 4 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

sumatra

??? missing short description for package sumatra :-(

http://metabarcoding.org/sumatra

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package sumatra
Release	Version	Architectures
trixie	1.0.36+ds-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	1.0.36+ds-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.0.36+ds-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.0.36+ds-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.0.36+ds-1	amd64,arm64,armhf,i386

Popcon: 6 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: SciCrunch

sumtrees

??? missing short description for package sumtrees :-(

https://jeetsukumaran.github.io/DendroPy

Maintainer: Debian Med Packaging Team (Ananthu C V)

Versions of package sumtrees
Release	Version	Architectures
sid	4.6.1-2	all
trixie	4.6.1-2	all
bookworm	4.5.2-1	all
bullseye	4.5.1-1	all
forky	4.6.1-2	all
upstream	5.0.8

Popcon: 7 users (34 upd.)^*

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Official Debian package

Git

Please cite: Jeet Sukumaran and Mark T. Holder: DendroPy: a Python library for phylogenetic computing. (PubMed,eprint) Bioinformatics 26(12):1569-1571 (2010)

surankco

??? missing short description for package surankco :-(

https://sourceforge.net/projects/surankco/

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package surankco
Release	Version	Architectures
forky	0.0.r5+dfsg-5	all
bookworm	0.0.r5+dfsg-3	all
bullseye	0.0.r5+dfsg-3	all
trixie	0.0.r5+dfsg-4	all
sid	0.0.r5+dfsg-5	all

Popcon: 4 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Mathias Kuhring, Piotr Wojtek Dabrowski, Vitor C. Piro, Andreas Nitsche and Bernhard Y. Renard: SuRankCo: supervised ranking of contigs in de novo assemblies. (PubMed,eprint) BMC Bioinformatics 16(1):240 (2015)

surpyvor

??? missing short description for package surpyvor :-(

https://github.com/wdecoster/surpyvor

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Popcon: 5 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

survivor

??? missing short description for package survivor :-(

https://github.com/fritzsedlazeck/SURVIVOR

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package survivor
Release	Version	Architectures
bullseye	1.0.7-2	amd64,arm64,armhf,i386
bookworm	1.0.7-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	1.0.7-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.0.7-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	1.0.7-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 5 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

svim

??? missing short description for package svim :-(

https://github.com/eldariont/svim

Maintainer: Debian Med Packaging Team (Andreas Tille)

Popcon: 6 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: David Heller and Martin Vingron: Link to publication (PubMed,eprint) Bioinformatics 35(17):2907-2915 (2019)

Registry entries: Bioconda

swarm

??? missing short description for package swarm :-(

https://github.com/torognes/swarm

Maintainer: Debian Med Packaging Team (Lance Lin)

Versions of package swarm
Release	Version	Architectures
bullseye	3.0.0+dfsg-2	amd64
forky	3.1.6+dfsg-1	amd64,arm64,ppc64el
sid	3.1.6+dfsg-1	amd64,arm64,ppc64el
trixie	3.1.5+dfsg-2	amd64,arm64,ppc64el
bookworm	3.1.2+dfsg-1	amd64,arm64,ppc64el

Popcon: 5 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Frédéric Mahé, Torbjørn Rognes, Christopher Quince, Colomban de Vargas and Micah Dunthorn: Swarm v2: highly-scalable and high-resolution amplicon clustering. (PubMed,eprint) PeerJ 3(e1420) (2015)

Registry entries: Bio.tools

sweed

??? missing short description for package sweed :-(

https://sco.h-its.org/exelixis/web/software/sweed/

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package sweed
Release	Version	Architectures
forky	3.2.1+dfsg-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	3.2.1+dfsg-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	3.2.1+dfsg-5	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	3.2.1+dfsg-5	amd64,arm64,armhf,i386
sid	3.2.1+dfsg-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 4 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Pavlos Pavlidis, Daniel Živković, Alexandros Stamatakis and Nikolaos Alachiotis: SweeD: Likelihood-Based Detection of Selective Sweeps in Thousands of Genomes. (eprint) Molecular Biology and Evolution 30(9):2224–2234 (2013)

Registry entries: Bio.tools

t-coffee

??? missing short description for package t-coffee :-(

https://www.tcoffee.org/Projects/tcoffee/index.html

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package t-coffee
Release	Version	Architectures
forky	13.45.0.4846264+really13.41.0.28bdc39+dfsg-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	13.45.0.4846264+really13.41.0.28bdc39+dfsg-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	13.45.0.4846264+really13.41.0.28bdc39+dfsg-1	amd64,arm64,armel,armhf,i386,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,armhf,i386

Debtags of package t-coffee:
field	biology, biology:bioinformatics
interface	commandline
role	program
scope	utility
use	analysing, comparing
works-with-format	plaintext

Popcon: 14 users (37 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: clustalw dialign-tx kalign mafft muscle muscle3 ncbi-blast+ poa prank probcons tm-align

Please cite: Cédric Notredame, Desmond G. Higgins and Jaap Heringa: T-coffee: a novel method for fast and accurate multiple sequence alignment. (PubMed) Journal of Molecular Biology 302(1):205-217 (2000)

Registry entries: Bio.tools SciCrunch Bioconda

tabix

??? missing short description for package tabix :-(

https://github.com/samtools/htslib

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package tabix
Release	Version	Architectures
trixie	1.21+ds-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	1.11-4	amd64,arm64,armhf,i386
sid	1.22.1+ds2-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.16+ds-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	1.22.1+ds2-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
upstream	1.23.1

Popcon: 40 users (63 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Heng Li: Tabix: fast retrieval of sequence features from generic TAB-delimited files. (PubMed,eprint) Bioinformatics 27(5):718-719 (2011)

Registry entries: Bio.tools Bioconda

tantan

??? missing short description for package tantan :-(

https://gitlab.com/mcfrith/tantan

Maintainer: Debian Med Packaging Team (Sascha Steinbiss)

Versions of package tantan
Release	Version	Architectures
bullseye	23-1	amd64,arm64,armhf,i386
bookworm	40-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	51-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	51-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	51-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 5 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Frith, Martin C.: A new repeat-masking method enables specific detection of homologous sequences. (PubMed) Nucleic Acids Research 39(4):e23 (2011)

Registry entries: Bioconda

Topics: Sequence composition, complexity and repeats

terraphast

??? missing short description for package terraphast :-(

https://github.com/amkozlov/terraphast-one

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package terraphast
Release	Version	Architectures
bookworm	0.0+git20200413.8af2e4c+dfsg-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	0.1.0+dfsg-1	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
sid	0.1.0+dfsg-1	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
trixie	0.0+git20200413.8af2e4c+dfsg-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 7 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Michael J. Sanderson, Michelle M. McMahon and Mike Steel: Terraces in phylogenetic tree space. (PubMed) Science 333(6041):448-450 (2011)

theseus

??? missing short description for package theseus :-(

http://www.theseus3d.org

Maintainer: Debian Med Packaging Team (Sergio Durigan Junior)

Versions of package theseus
Release	Version	Architectures
bookworm	3.3.0-14	amd64,i386
trixie	3.3.0-14	amd64,i386
bullseye	3.3.0-9	amd64,arm64,armhf,i386
forky	3.3.0-15	amd64,i386
sid	3.3.0-15	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

Popcon: 9 users (35 upd.)^*

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License: DFSG free

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Git

The package is enhanced by the following packages: theseus-examples

Please cite: Douglas L. Theobald and Deborah S. Wuttke: THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures. (eprint) Bioinformatics 22(17):2171-2172 (2006)

thesias

??? missing short description for package thesias :-(

https://github.com/daissi/thesias

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package thesias
Release	Version	Architectures
bookworm	3.1.1-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	3.1.1-4	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
bullseye	3.1.1-1	amd64,arm64,armhf,i386
trixie	3.1.1-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	3.1.1-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 7 users (32 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: David-Alexandre Trégouët and Valérie Garelle: "A new JAVA interface implementation of THESIAS: testing haplotype effects in association studies". (eprint) Bioinformatics 23(8):1038-1039 (2007)

Registry entries: Bio.tools SciCrunch Bioconda

tiddit

??? missing short description for package tiddit :-(

https://github.com/SciLifeLab/TIDDIT

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package tiddit
Release	Version	Architectures
bullseye	2.12.0+dfsg-3	amd64,arm64,armhf,i386
bookworm	3.5.2+dfsg-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el
trixie	3.6.1+dfsg-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64
forky	3.6.1+dfsg-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
sid	3.6.1+dfsg-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
upstream	3.9.5

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License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools Bioconda

tigr-glimmer

??? missing short description for package tigr-glimmer :-(

http://ccb.jhu.edu/software/glimmer/index.shtml

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package tigr-glimmer
Release	Version	Architectures
bookworm	3.02b-6	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	3.02b-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	3.02b-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	3.02b-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	3.02b-5	amd64,arm64,armhf,i386

Debtags of package tigr-glimmer:
field	biology, biology:bioinformatics
interface	commandline
role	program
scope	utility
use	searching
works-with-format	plaintext

Popcon: 14 users (33 upd.)^*

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License: DFSG free

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Git

Please cite: Steven L. Salzberg, Arthur L. Delcher, S. Kasif and O. White: Microbial gene identification using interpolated Markov models. (PubMed,eprint) Nucleic Acids Research 26(2):544-8 (1998)

Registry entries: Bio.tools SciCrunch Bioconda

tipp

??? missing short description for package tipp :-(

https://github.com/TeraTrees/TIPP

Maintainer: Debian Med Packaging Team (Santiago Vila)

Popcon: users ( upd.)^*

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License: DFSG free

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tm-align

??? missing short description for package tm-align :-(

https://zhanglab.ccmb.med.umich.edu/TM-align/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package tm-align
Release	Version	Architectures
bookworm	20190822+dfsg-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	20190822+dfsg-2	amd64,arm64,armhf,i386
trixie	20190822+dfsg-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	20190822+dfsg-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	20190822+dfsg-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

Please cite: Yang Zhang and Jeffrey Skolnick: TM-align: A protein structure alignment algorithm based on TM-score. (PubMed,eprint) Nucleic Acids Research 33(7):2302-2309 (2005)

tnseq-transit

??? missing short description for package tnseq-transit :-(

http://saclab.tamu.edu/essentiality/transit/

Maintainer: Debian Med Packaging Team (Alexandre Detiste)

Versions of package tnseq-transit
Release	Version	Architectures
trixie	3.3.12-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	3.3.12-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	3.2.1-1	amd64,arm64,armhf,i386
bookworm	3.2.7-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream	3.3.20

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License: DFSG free

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Git

Please cite: Michael A. DeJesus, Chaitra Ambadipudi, Richard Baker, Christopher Sassetti and Thomas R. Ioerger: TRANSIT - A Software Tool for Himar1 TnSeq Analysis. (PubMed,eprint) PLOS 11(10):e1004401 (2015)

Registry entries: Bio.tools Bioconda

toil

??? missing short description for package toil :-(

https://github.com/DataBiosphere/toil

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package toil
Release	Version	Architectures
forky	9.3.0-3	all
bullseye	5.2.0-5	all
sid	9.4.1-1	all
trixie	8.0.0-5	all
trixie-proposed-updates	8.0.0-5+deb13u1	all
bookworm	5.9.2-2+deb12u1	all

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License: DFSG free

Official Debian package

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Please cite: John Vivian, Arjun Arkal Rao, Frank Austin Nothaft, Christopher Ketchum, Joel Armstrong, Adam Novak, Jacob Pfeil, Jake Narkizian Alden D. Deran, Audrey Musselman-Brown, Hannes Schmidt, Peter Amstutz, Brian Craft, Mary Goldman, Kate Rosenbloom, Melissa Cline, Brian O'Connor, Megan Hanna, Chet Birger, W. James Kent David A. Patterson, Anthony D. Joseph, Jingchun Zhu, Sasha Zaranek, Gad Getz, David Haussler and Benedict Paten: Toil enables reproducible, open source, big biomedical data analyses. Nature Biotechnology 35(4):314–316 (2017)

Registry entries: Bioconda

tombo

??? missing short description for package tombo :-(

https://github.com/nanoporetech/tombo

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package tombo
Release	Version	Architectures
sid	1.5.1-9	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.5.1-2	amd64,arm64,armhf,i386
trixie	1.5.1-7	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.5.1-8	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.5.1-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 5 users (36 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Marcus Stoiber, Joshua Quick, Rob Egan, Ji Eun Lee, Susan Celniker, Robert K. Neely, Nicholas Loman, Len A Pennacchio and James Brown: De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing. (eprint) bioRxiv (2016)

Registry entries: Bioconda

tophat-recondition

??? missing short description for package tophat-recondition :-(

https://github.com/cbrueffer/tophat-recondition

Maintainer: Debian Med Packaging Team (Steffen Moeller)

Popcon: 6 users (33 upd.)^*

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License: DFSG free

Official Debian package

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Please cite: Christian Brueffer and Lao H. Saal: A post-processor for TopHat unmapped reads. Bioinformatics 17(1):199 (2016)

Registry entries: Bio.tools Bioconda

topp

??? missing short description for package topp :-(

https://www.openms.de

Maintainer: The Debichem Group (Santiago Vila)

Versions of package topp
Release	Version	Architectures
sid	2.6.0+cleaned1-6	amd64,arm64,i386,loong64,ppc64el,riscv64,s390x
bookworm	2.6.0+cleaned1-3	amd64,arm64,i386,mips64el,mipsel,ppc64el,s390x
trixie	2.6.0+cleaned1-4	amd64,arm64,i386,ppc64el,riscv64,s390x
forky	2.6.0+cleaned1-6	amd64,arm64,i386,ppc64el,riscv64,s390x
bullseye	2.6.0+cleaned1-3	amd64,arm64,i386
upstream	2.9.1

Popcon: 13 users (33 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools SciCrunch Bioconda

toppred

??? missing short description for package toppred :-(

https://github.com/bioinfo-center-pasteur-fr/toppred

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package toppred
Release	Version	Architectures
forky	1.10-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.10-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.10-10	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.10-8	amd64,arm64,armhf,i386
trixie	1.10-10	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 4 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Gunnar von Heijne: Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. (PubMed) Journal of Molecular Biology 225(2):487-94 (1992)

tortoize

??? missing short description for package tortoize :-(

https://github.com/PDB-REDO/tortoize

Maintainer: Debian Med Packaging Team (Maarten L. Hekkelman)

Versions of package tortoize
Release	Version	Architectures
sid	2.0.16-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	2.0.15-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	2.0.16-1	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
bookworm	2.0.11-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	2.0.1-2	amd64,arm64,armhf,i386

Popcon: 4 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Oleg V. Sobolev, Pavel V. Afonine, Nigel W. Moriarty and Robbie P. Joosten: A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry, Structure. (2020)

trace2dbest

??? missing short description for package trace2dbest :-(

http://www.nematodes.org/bioinformatics/trace2dbEST/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package trace2dbest
Release	Version	Architectures
bookworm	3.0.1-2	all
bullseye	3.0.1-2	all
sid	3.0.1-2	all
forky	3.0.1-2	all
trixie	3.0.1-2	all

Popcon: 3 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: John Parkinson, Alasdair Anthony, James Wasmuth, Ralf Schmid, Ann Hedley and Mark Blaxter: PartiGene—constructing partial genomes. (eprint) Bioinformatics 20(9):1398–1404 (2004)

tracetuner

??? missing short description for package tracetuner :-(

https://sourceforge.net/projects/tracetuner/

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package tracetuner
Release	Version	Architectures
sid	3.0.6~beta+dfsg-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	3.0.6~beta+dfsg-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	3.0.6~beta+dfsg-3	amd64,arm64,armhf,i386
trixie	3.0.6~beta+dfsg-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	3.0.6~beta+dfsg-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 6 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: G.A.Denisov, A.B.Arehart and M.D.Curtin: A system and method for improving the accuracy of DNA sequencing and error probability estimation through application of a mathematical model to the analysis of electropherograms. US Patent 6681186. (2004)

Registry entries: SciCrunch

transdecoder

??? missing short description for package transdecoder :-(

https://transdecoder.github.io/

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Popcon: 6 users (36 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

transrate-tools

??? missing short description for package transrate-tools :-(

https://hibberdlab.com/transrate/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package transrate-tools
Release	Version	Architectures
bookworm	1.0.0-5	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.0.0-3	amd64,arm64,armhf,i386
trixie	1.0.0-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.0.0-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.0.0-7	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 5 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Richard Smith-Unna, Chris Boursnell, Rob Patro, Julian M. Hibberd and Steven Kelly: TransRate: reference-free quality assessment of de novo transcriptome assemblies.. (PubMed,eprint) Genome Research 26(8):1134-1144 (2016)

Registry entries: Bioconda

transtermhp

??? missing short description for package transtermhp :-(

https://transterm.cbcb.umd.edu/

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package transtermhp
Release	Version	Architectures
forky	2.09-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	2.09-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	2.09-5	amd64,arm64,armhf,i386
bookworm	2.09-5	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	2.09-5	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 6 users (33 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Carleton L Kingsford, Kunmi Ayanbule and Steven L Salzberg: Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. (PubMed,eprint) Genome Biology 8(2):R22 (2007)

Registry entries: SciCrunch Bioconda

tree-ppuzzle

??? missing short description for package tree-ppuzzle :-(

http://www.tree-puzzle.de

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package tree-ppuzzle
Release	Version	Architectures
forky	5.3~rc16+dfsg-14	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
trixie	5.3~rc16+dfsg-12	amd64,arm64,armel,armhf,i386,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,armhf,i386
sid	5.3~rc16+dfsg-14	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Debtags of package tree-ppuzzle:
field	biology, biology:bioinformatics
interface	commandline
role	program
scope	utility
use	analysing, comparing
works-with-format	plaintext

Popcon: 1 users (0 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Heiko A. Schmidt, Korbinian Strimmer, Martin Vingron and Arndt von Haeseler: TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. (PubMed,eprint) Bioinformatics 18(3):502-504 (2002)

Registry entries: Bio.tools

tree-puzzle

??? missing short description for package tree-puzzle :-(

http://www.tree-puzzle.de

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package tree-puzzle
Release	Version	Architectures
bookworm	5.3~rc16+dfsg-9	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	5.3~rc16+dfsg-14	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
sid	5.3~rc16+dfsg-14	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	5.3~rc16+dfsg-12	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	5.3~rc16+dfsg-8	amd64,arm64,armhf,i386

Debtags of package tree-puzzle:
field	biology, biology:bioinformatics
interface	commandline
role	program
scope	utility
use	analysing, comparing
works-with-format	plaintext

Popcon: 8 users (36 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools

treeview

??? missing short description for package treeview :-(

https://jtreeview.sourceforge.net

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package treeview
Release	Version	Architectures
bullseye	1.2.0+dfsg-1	all
bookworm	1.2.0+dfsg-1	all
trixie	1.2.0+dfsg-2	all
forky	1.2.0+dfsg-2	all
sid	1.2.0+dfsg-2	all
upstream	1.2.1

Popcon: 5 users (34 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: Alok J. Saldanha: Java Treeview -- extensible visualization of microarray data. (PubMed,eprint) Bioinformatics 20(17):3246-3248 (2004)

Registry entries: Bio.tools SciCrunch

treeviewx

??? missing short description for package treeviewx :-(

https://github.com/rdmpage/treeviewx

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package treeviewx
Release	Version	Architectures
sid	0.5.1+git20100823.7e4d0e9-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	0.5.1+git20100823.7e4d0e9-4	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
trixie	0.5.1+git20100823.7e4d0e9-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	0.5.1+git20100823.7e4d0e9-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	0.5.1+git20100823.7e4d0e9-3	amd64,arm64,armhf,i386

Debtags of package treeviewx:
field	biology, biology:bioinformatics
interface	x11
role	program
scope	utility
uitoolkit	wxwidgets
use	viewing
works-with-format	pdf, plaintext, postscript, svg
x11	application

Popcon: 7 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Page, Roderic D. M.: TreeView: an application to display phylogenetic trees on personal computers. (PubMed) Comput. Appl. Biosci. 12(4):357-8 (1996)

Registry entries: Bio.tools

trf

??? missing short description for package trf :-(

https://tandem.bu.edu/trf/trf.html

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package trf
Release	Version	Architectures
bullseye	4.09.1-4	amd64,arm64,armhf,i386
bookworm	4.09.1-6	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	4.09.1-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	4.09.1-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	4.09.1-6	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 4 users (33 upd.)^*

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License: DFSG free

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Git

The package is enhanced by the following packages: trf-examples

Please cite: Gary Benson: Tandem repeats finder: a program to analyze DNA sequences. (PubMed,eprint) Nucleic Acids Research 27(2):573–580 (1999)

Registry entries: Bioconda

trim-galore

??? missing short description for package trim-galore :-(

https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package trim-galore
Release	Version	Architectures
bullseye	0.6.6-1	all
bookworm	0.6.10-1	all
trixie	0.6.10-1	all
forky	0.6.10-1	all
sid	0.6.10-1	all
upstream	2.2.0

Popcon: 5 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools Bioconda

trimmomatic

??? missing short description for package trimmomatic :-(

http://www.usadellab.org/cms/index.php?page=trimmomatic

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package trimmomatic
Release	Version	Architectures
bullseye	0.39+dfsg-2	all
bookworm	0.39+dfsg-2	all
trixie	0.39+dfsg-2	all
forky	0.39+dfsg-2	all
sid	0.39+dfsg-2	all

Popcon: 8 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: multiqc

Please cite: A.M. Bolger, M. Lohse and B. Usadel: Trimmomatic: a flexible trimmer for Illumina sequence data. (PubMed,eprint) Bioinformatics 30(15):2114-2120 (2014)

Registry entries: Bio.tools SciCrunch Bioconda

Topics: Sequencing

trinityrnaseq

??? missing short description for package trinityrnaseq :-(

https://github.com/trinityrnaseq/trinityrnaseq

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package trinityrnaseq
Release	Version	Architectures
trixie	2.15.2+dfsg-1	amd64,arm64,ppc64el,riscv64
bullseye	2.11.0+dfsg-6	amd64,arm64
sid	2.15.2+dfsg-3	amd64,arm64,loong64,ppc64el,riscv64

Popcon: 8 users (30 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Manfred G Grabherr, Brian J Haas, Moran Yassour, Joshua Z Levin, Dawn A Thompson, Ido Amit, Xian Adiconis, Lin Fan, Raktima Raychowdhury, Qiandong Zeng, Zehua Chen, Evan Mauceli, Nir Hacohen, Andreas Gnirke, Nicholas Rhind, Federica di Palma, Bruce W Birren, Chad Nusbaum, Kerstin Lindblad-Toh, Nir Friedman and Aviv Regev: Full-length transcriptome assembly from RNA-Seq data without a reference genome.. (PubMed) Nature Biotechnology 29(7):644-652 (2011)

Registry entries: Bio.tools SciCrunch Bioconda

tvc

??? missing short description for package tvc :-(

http://ioncommunity.thermofisher.com

Maintainer: Debian Med Packaging Team (Mohammed Bilal)

Versions of package tvc
Release	Version	Architectures
bookworm	5.0.3+git20151221.80e144e+dfsg-5	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	5.0.3+git20151221.80e144e+dfsg-3	amd64,arm64,armhf,i386
trixie	5.0.3+git20151221.80e144e+dfsg-5	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

twopaco

??? missing short description for package twopaco :-(

https://github.com/medvedevgroup/TwoPaCo

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package twopaco
Release	Version	Architectures
sid	1.0.0+dfsg-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.0.0+dfsg-1	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
forky	1.0.0+dfsg-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.0.0+dfsg-1	amd64,arm64,armhf,i386,mips64el,ppc64el,s390x
upstream	1.1.0

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Official Debian package

Git

Please cite: Ilia Minkin, Son Pham and Paul Medvedev: TwoPaCo: an efficient algorithm to build the compacted de Bruijn graph from many complete genomes. (PubMed,eprint) Bioinformatics 33(24):4024-4032 (2017)

Registry entries: Bioconda

uc-echo

??? missing short description for package uc-echo :-(

https://uc-echo.sourceforge.net/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package uc-echo
Release	Version	Architectures
forky	1.12-19	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.12-18	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.12-15	amd64,arm64,armhf,i386
sid	1.12-19	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.12-19	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

Please cite: W.-C. Kao, A.H. Chan and Y.S. Song: ECHO: A reference-free short-read error correction algorithm. (PubMed,eprint) Genome Research 21:1181-1192 (2011)

Registry entries: Bio.tools SciCrunch

Topics: Data management; Sequencing

ugene

??? missing short description for package ugene :-(

https://ugene.unipro.ru

Maintainer: Debian Med Packaging Team (Pierre Gruet)

Versions of package ugene
Release	Version	Architectures
bullseye	34.0+dfsg-2 (non-free)	amd64
trixie	51.0+dfsg-3	amd64,arm64
forky	52.1+dfsg-1	amd64,arm64
sid	52.1+dfsg-1	amd64,arm64
upstream	53.1

Popcon: 5 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Konstantin Okonechnikov, Olga Golosova, Mikhail Fursov and the UGENE team: Unipro UGENE: a unified bioinformatics toolkit. (PubMed,eprint) Bioinformatics 28(8):1166-1167 (2012)

Registry entries: Bio.tools SciCrunch

umap-learn

??? missing short description for package umap-learn :-(

https://github.com/lmcinnes/umap

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package umap-learn
Release	Version	Architectures
bullseye	0.4.5+dfsg-2	all
bookworm	0.5.3+dfsg-2	all
sid	0.5.9.post2+dfsg-1	all
upstream	0.5.12

Popcon: 2 users (1 upd.)^*

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Please cite: Leland McInnes, John Healy and James Melville: UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction. (eprint) arXiv (2018)

umis

??? missing short description for package umis :-(

https://github.com/vals/umis

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package umis
Release	Version	Architectures
bookworm	1.0.8-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el
bullseye	1.0.7-1	amd64,arm64,armhf,i386
sid	1.0.9-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64

Popcon: 1 users (0 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Valentine Svensson, Kedar Nath Natarajan, Lam-Ha Ly, Ricardo J Miragaia, Charlotte Labalette, Iain C Macaulay, Ana Cvejic and Sarah A Teichmann: Power analysis of single-cell RNA-sequencing experiments. (PubMed) Nature methods 14:381–387 (2017)

Registry entries: Bioconda

uncalled

??? missing short description for package uncalled :-(

https://github.com/skovaka/UNCALLED

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package uncalled
Release	Version	Architectures
trixie	2.3+ds-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	2.2+ds1-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	2.2+ds-1	amd64,arm64,armhf,i386
forky	2.3+ds-3	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
sid	2.3+ds-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 5 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Sam Kovaka, Yunfan Fan, Bohan Ni, Winston Timp and Michael C. Schatz: Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED. (eprint) Nature Biotechnology (2020)

unicycler

??? missing short description for package unicycler :-(

https://github.com/rrwick/Unicycler

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package unicycler
Release	Version	Architectures
trixie	0.5.1+dfsg-3	amd64
sid	0.5.1+dfsg-4	amd64
bookworm	0.5.0+dfsg-1	amd64
bullseye	0.4.8+dfsg-2	amd64

Popcon: 6 users (32 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Ryan R. Wick, Louise M. Judd, Claire L. Gorrie and Kathryn E. Holt: Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. (PubMed,eprint) PLOS Computational Biology 13(6):e1005595 (2017)

Registry entries: Bio.tools Bioconda

unikmer

??? missing short description for package unikmer :-(

https://github.com/shenwei356/unikmer

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package unikmer
Release	Version	Architectures
bookworm	0.19.1-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	0.20.0-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	0.20.0-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	0.20.0-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 5 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

varna

??? missing short description for package varna :-(

https://varna.lri.fr/

Maintainer: Debian Med Packaging Team (Pierre Gruet)

Versions of package varna
Release	Version	Architectures
bookworm	3-93+ds-4	all
trixie	3-93+ds-7	all
forky	3-93+ds-7	all
sid	3-93+ds-7	all
bullseye	3-93+ds-3	all

Popcon: 6 users (35 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Kévin Darty, Alain Denise and Yann Ponty: VARNA: Interactive drawing and editing of the RNA secondary structure. (eprint) Bioinformatics 25(15):1974-1975 (2009)

vcfanno

??? missing short description for package vcfanno :-(

https://github.com/brentp/vcfanno

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package vcfanno
Release	Version	Architectures
sid	0.3.7+ds-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	0.3.5+ds-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	0.3.5+ds-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	0.3.7+ds-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	0.3.2+ds-2	amd64,arm64,armhf,i386
upstream	0.3.8

Popcon: 6 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Brent S. Pedersen, Ryan M. Layer and Aaron R. Quinlan: Vcfanno: fast, flexible annotation of genetic variants. (PubMed,eprint) Genome Biology 17(1):118 (2016)

Registry entries: Bio.tools Bioconda

vcftools

??? missing short description for package vcftools :-(

https://vcftools.github.io/

Maintainer: Debian Med Packaging Team (Dylan Aïssi)

Versions of package vcftools
Release	Version	Architectures
bookworm	0.1.16-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	0.1.17-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	0.1.17-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	0.1.16-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	0.1.16-2	amd64,arm64,armhf,i386

Popcon: 21 users (34 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

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)

Registry entries: Bio.tools SciCrunch Bioconda

velvet

??? missing short description for package velvet :-(

https://github.com/dzerbino/velvet

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package velvet
Release	Version	Architectures
forky	1.2.10+dfsg1-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.2.10+dfsg1-9	amd64,arm64,armel,armhf,i386,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,armhf,i386
sid	1.2.10+dfsg1-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 7 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Daniel R. Zerbino and Ewan Birney: Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. (PubMed,eprint) Genome Research 18(5):821-829 (2008)

Registry entries: Bio.tools SciCrunch Bioconda

velvet-long

??? missing short description for package velvet-long :-(

https://github.com/dzerbino/velvet

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package velvet-long
Release	Version	Architectures
trixie	1.2.10+dfsg1-9	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.2.10+dfsg1-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	1.2.10+dfsg1-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.2.10+dfsg1-10	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.2.10+dfsg1-7	amd64,arm64,armhf,i386

Popcon: 0 users (0 upd.)^*

Versions and Archs

License: DFSG free

Official Debian package

Git

Please cite: Daniel R. Zerbino and Ewan Birney: Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. (PubMed,eprint) Genome Research 18(5):821-829 (2008)

Registry entries: Bio.tools SciCrunch Bioconda

velvetoptimiser

??? missing short description for package velvetoptimiser :-(

https://github.com/tseemann/VelvetOptimiser/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package velvetoptimiser
Release	Version	Architectures
trixie	2.2.6-5	all
forky	2.2.6-5	all
sid	2.2.6-5	all
bullseye	2.2.6-3	all
bookworm	2.2.6-5	all

Popcon: 5 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools Bioconda

veryfasttree

??? missing short description for package veryfasttree :-(

https://github.com/citiususc/veryfasttree

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package veryfasttree
Release	Version	Architectures
sid	4.0.5+dfsg-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	4.0.5+dfsg-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	4.0.4+dfsg-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 5 users (34 upd.)^*

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License: DFSG free

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Git

??? missing short description for package vg :-(

https://github.com/vgteam/vg#vg

Maintainer: Debian Med Packaging Team (Bastian Germann)

Popcon: 0 users (0 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Erik Garrison, Jouni Sirén, Adam M Novak, Glenn Hickey, Jordan M Eizenga, Eric T Dawson, William Jones, Shilpa Garg, Charles Markello, Michael F Lin, Benedict Paten and Richard Durbin: Variation graph toolkit improves read mapping by representing genetic variation in the reference. (PubMed) Nature Biotechnology 36(9):875–879 (2018)

Registry entries: Bioconda

virulencefinder

??? missing short description for package virulencefinder :-(

https://bitbucket.org/genomicepidemiology/virulencefinder

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package virulencefinder
Release	Version	Architectures
forky	2.0.5-2	all
sid	2.0.5-2	all
bullseye	2.0.3+git20190809.dde157a-3	all
bookworm	2.0.4-3	all
trixie	2.0.5-2	all
upstream	3.2.0

Popcon: 5 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Katrine Grimstrup Joensen, Flemming Scheutz, Ole Lund, Henrik Hasman, Rolf S. Kaas, Eva M. Nielsen and Frank M. Aarestrup: Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli. (PubMed,eprint) Journal of Clinical Microbiology 52(5):1501-10 (2014)

vmatch

??? missing short description for package vmatch :-(

http://www.vmatch.de

Maintainer: Debian Med Packaging Team (Sascha Steinbiss)

Versions of package vmatch
Release	Version	Architectures
sid	2.3.1+git20240412.b3b8ac0+dfsg-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	2.3.1+dfsg-9	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	2.3.1+dfsg-6	amd64,arm64,armhf,i386
bookworm	2.3.1+dfsg-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	2.3.1+git20240412.b3b8ac0+dfsg-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 7 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools Bioconda

vsearch

??? missing short description for package vsearch :-(

https://github.com/torognes/vsearch/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package vsearch
Release	Version	Architectures
trixie	2.30.0-1	amd64,arm64,ppc64el,riscv64
sid	2.30.4-1	amd64,arm64,loong64,ppc64el,riscv64
forky	2.30.4-1	amd64,arm64,loong64,ppc64el,riscv64
bookworm	2.22.1-1	amd64,arm64,ppc64el
bullseye	2.15.2-3	amd64,arm64
upstream	2.31.0

Popcon: 8 users (35 upd.)^*

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License: DFSG free

Official Debian package

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The package is enhanced by the following packages: vsearch-examples

Please cite: Torbjørn Rognes, Tomáš Flouri, Ben Nichols, Christopher Quince and Frédéric Mahé: VSEARCH: a versatile open source tool for metagenomics. (eprint) PeerJ 4:e2584

Registry entries: Bio.tools Bioconda

??? missing short description for package vt :-(

https://genome.sph.umich.edu/wiki/Vt

Maintainer: Debian Med Packaging Team (Antoni Villalonga)

Versions of package vt
Release	Version	Architectures
bookworm	0.57721+ds-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	0.57721+ds-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	0.57721+ds-3	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
trixie	0.57721+ds-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	0.57721+ds-3	amd64,arm64,armhf,i386

Popcon: 5 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: vt-examples

Please cite: Adrian Tan, Gonçalo R. Abecasis and Hyun Min Kang: Unified representation of genetic variants. (PubMed,eprint) Bioinformatics 31(13):2202–2204 (2015)

Registry entries: Bio.tools Bioconda

wham-align

??? missing short description for package wham-align :-(

http://research.cs.wisc.edu/wham

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package wham-align
Release	Version	Architectures
sid	0.1.5-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	0.1.5-8	amd64,arm64,armhf,i386
bookworm	0.1.5-8	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	0.1.5-8	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	0.1.5-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 6 users (32 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Yinan Li, Allie Terrell and Jignesh M. Patel: WHAM: A High-throughput Sequence Alignment Method (eprint) Proceedings of the ACM SIGMOD International Conference on Management of Data, SIGMOD 2011, Athens, Greece (2011)

Registry entries: Bio.tools SciCrunch Bioconda

wigeon

??? missing short description for package wigeon :-(

https://microbiomeutil.sourceforge.net/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package wigeon
Release	Version	Architectures
forky	20101212+dfsg1-6	all
bullseye	20101212+dfsg1-4	all
bookworm	20101212+dfsg1-5	all
trixie	20101212+dfsg1-6	all
sid	20101212+dfsg1-6	all

Popcon: 6 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: microbiomeutil-data

Registry entries: SciCrunch

wise

??? missing short description for package wise :-(

https://www.ebi.ac.uk/~birney/wise2/

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package wise
Release	Version	Architectures
sid	2.4.1-28	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	2.4.1-23	amd64,arm64,armhf,i386
bookworm	2.4.1-23	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	2.4.1-27	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	2.4.1-28	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 20 users (38 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Ewan Birney, Michele Clamp and Richard Durbin: GeneWise and Genomewise. (PubMed,eprint) Genome Research 14(5):988-95 (2004)

Registry entries: Bio.tools Bioconda

xpore

??? missing short description for package xpore :-(

https://github.com/GoekeLab/xpore/

Maintainer: Debian Med Packaging Team (Komolehin Israel Timilehin)

Popcon: 6 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

yaha

??? missing short description for package yaha :-(

https://github.com/GregoryFaust/yaha

Maintainer: Debian Med Packaging Team (Shruti Sridhar)

Versions of package yaha
Release	Version	Architectures
bullseye	0.1.83-2	amd64,arm64,armhf,i386
bookworm	0.1.83-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	0.1.83-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	0.1.83-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	0.1.83-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 5 users (33 upd.)^*

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License: DFSG free

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Git

Please cite: Gregory G. Faust and Ira M. Hall: YAHA: fast and flexible long-read alignment with optimal breakpoint detection. (PubMed,eprint) Bioinformatics 28(19):2417–2424 (2012)

Registry entries: Bioconda

yanagiba

??? missing short description for package yanagiba :-(

https://github.com/Adamtaranto/Yanagiba

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Popcon: 7 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

yanosim

??? missing short description for package yanosim :-(

https://github.com/bartongroup/yanosim

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package yanosim
Release	Version	Architectures
forky	0.1-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
trixie	0.1-6	amd64,arm64,armel,armhf,i386,ppc64el,riscv64
bookworm	0.1-5	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el
sid	0.1-8	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
bullseye	0.1-3	amd64,arm64,armhf,i386

Popcon: 5 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Official Debian packages with lower relevance

adun.app

??? missing short description for package adun.app :-(

http://wiki.gnustep.org/index.php/Adun

Maintainer: Debian Med Packaging Team (Yavor Doganov)

Versions of package adun.app
Release	Version	Architectures
bullseye	0.81-14	amd64,arm64,armhf,i386
forky	0.81-15	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
trixie	0.81-15	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	0.81-14	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	0.81-15	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Debtags of package adun.app:
field	biology, biology:structural
interface	x11
role	program
scope	application
suite	gnustep
uitoolkit	gnustep
use	analysing, organizing, viewing
works-with	3dmodel, db
x11	application

Popcon: 6 users (3 upd.)^*

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License: DFSG free

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catfishq

??? missing short description for package catfishq :-(

https://github.com/philres/catfishq

Maintainer: Steffen Moeller (tony mancill)

Popcon: 0 users (0 upd.)^*

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License: DFSG free

Official Debian package

Git

conda-package-handling

??? missing short description for package conda-package-handling :-(

https://github.com/conda/conda-package-handling

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package conda-package-handling
Release	Version	Architectures
trixie	2.3.0-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	2.4.0-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	2.4.0-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	1.7.2-2+deb11u1	amd64,arm64,armhf,i386
bookworm	2.0.1-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 12 users (5 upd.)^*

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License: DFSG free

Official Debian package

Git

Remark of Debian Med team: Dead upstream

The homepage of this project vanished as well as the Download area. An old unmaintained version remained at code.google.com. Please drop the maintainer a note if you have any news of this project.

dascrubber

??? missing short description for package dascrubber :-(

https://dazzlerblog.wordpress.com/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package dascrubber
Release	Version	Architectures
bullseye	1.1-2	amd64,arm64,armhf,i386
sid	1.1-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	1.1-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.1-4	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.1-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 10 users (30 upd.)^*

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License: DFSG free

Official Debian package

Git

dnapi

??? missing short description for package dnapi :-(

https://github.com/jnktsj/DNApi/

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Popcon: 0 users (0 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Junko Tsuji and Zhiping Weng: DNApi: A De Novo Adapter Prediction Algorithm for Small RNA Sequencing Data. (PubMed,eprint) PLoS One 11(10):e0164228 (2016)

Registry entries: Bioconda

emboss-explorer

??? missing short description for package emboss-explorer :-(

http://embossgui.sourceforge.net/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package emboss-explorer
Release	Version	Architectures
sid	2.2.0-12	all
trixie	2.2.0-12	all
bullseye	2.2.0-11	all
bookworm	2.2.0-11	all
forky	2.2.0-12	all

Popcon: 0 users (0 upd.)^*

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License: DFSG free

Official Debian package

Git

getdata

??? missing short description for package getdata :-(

http://debian-med.alioth.debian.org

Maintainer: Debian Med Packaging Team (Andreas Tille)

Popcon: 3 users (0 upd.)^*

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License: DFSG free

Official Debian package

Git

hts-nim-tools

??? missing short description for package hts-nim-tools :-(

https://github.com/brentp/hts-nim-tools

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package hts-nim-tools
Release	Version	Architectures
forky	0.2.1-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
sid	0.2.1-4	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
bookworm	0.2.1-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el
bullseye	0.2.1-1	amd64,arm64,armhf,i386

Popcon: 0 users (0 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

idseq-bench

??? missing short description for package idseq-bench :-(

https://github.com/chanzuckerberg/idseq-bench

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package idseq-bench
Release	Version	Architectures
forky	0.0~git20210602.27fb6dc-2	all
sid	0.0~git20210602.27fb6dc-2	all
bookworm	0.0~git20210602.27fb6dc-1	all
bullseye	0.0~git20200902.8241a9a-1	all

Popcon: 0 users (0 upd.)^*

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License: DFSG free

Official Debian package

Git

illustrate

??? missing short description for package illustrate :-(

https://github.com/ccsb-scripps/Illustrate

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package illustrate
Release	Version	Architectures
forky	0.0+git20200923.217db48-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	0.0+git20200923.217db48-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	0.0+git20200923.217db48-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	0.0+git20200923.217db48-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
upstream	0.0+git20240817.e469df4

Popcon: 1 users (0 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: D.S. Goodsell and A.J. Olson: Molecular Illustration in Black and White. (PubMed) J. Mol. Graphics 10(4):235-240 (1992)

Registry entries: Bio.tools

libhdf5-dev

??? missing short description for package libhdf5-dev :-(

http://hdfgroup.org/HDF5/

Maintainer: Gilles Filippini

Versions of package libhdf5-dev
Release	Version	Architectures
trixie	1.14.5+repack-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	1.10.6+repack-4+deb11u1	amd64,arm64,armhf,i386
sid	1.14.6+repack-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
experimental	2.1.0+repack-1~exp3	riscv64
experimental	2.1.0+repack-1~exp6	amd64,arm64,armhf,i386,loong64,ppc64el,s390x
bookworm	1.10.8+repack1-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky	1.14.6+repack-2	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
upstream	2.1.0

Popcon: 350 users (495 upd.)^*

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License: DFSG free

Official Debian package

Git

libhnswlib-dev

??? missing short description for package libhnswlib-dev :-(

https://github.com/nmslib/hnswlib

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package libhnswlib-dev
Release	Version	Architectures
bullseye	0.4.0-3+deb11u1	all
bookworm	0.6.2-2+deb12u1	all
trixie	0.8.0-1	all
forky	0.9.0-1	all
sid	0.9.0-2	all

Popcon: 7 users (39 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Yu. A. Malkov and D. A. Yashunin: Efficient and robust approximate nearest neighbor search using Hierarchical Navigable Small World graphs. (eprint) arXiv.org arXiv(1603.0932) (2016)

maude

??? missing short description for package maude :-(

http://maude.cs.uiuc.edu

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package maude
Release	Version	Architectures
sid	3.5.1-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	3.2-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	3.4-1	amd64,arm64,ppc64el,riscv64,s390x
bullseye	3.1-2	amd64,arm64,armhf,i386
forky	3.5.1-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x

Popcon: 7 users (1 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: M. Matsumoto and T. Nishimura: Mersenne Twister: A 623-Dimensionally Equidistributed Uniform Pseudo-Random Number Generator. ACM Transactions on Modeling and Computer Simulation 8(1):3-30 (1998)

metastudent-data

??? missing short description for package metastudent-data :-(

https://rostlab.org/owiki/index.php/Metastudent

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package metastudent-data
Release	Version	Architectures
trixie	2.0.1-8	all
sid	2.0.1-9	all
forky	2.0.1-9	all
bookworm	2.0.1-8	all
bullseye	2.0.1-7	all

Popcon: 0 users (0 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools

metastudent-data-2

??? missing short description for package metastudent-data-2 :-(

https://rostlab.org/owiki/index.php/Metastudent

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package metastudent-data-2
Release	Version	Architectures
trixie	1.0.0-6	all
bullseye	1.0.0-5	all
bookworm	1.0.0-6	all
sid	1.0.0-6	all
forky	1.0.0-6	all

Popcon: 0 users (0 upd.)^*

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License: DFSG free

Official Debian package

Git

python3-anndata

??? missing short description for package python3-anndata :-(

https://github.com/theislab/anndata

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package python3-anndata
Release	Version	Architectures
sid	0.12.6-1	all
bookworm	0.8.0-4	all
bullseye	0.7.5+ds-3	all
upstream	0.12.14

Popcon: 0 users (0 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: F. Alexander Wolf, Philipp Angerer and Fabian J. Theis: SCANPY: large-scale single-cell gene expression data analysis.. (PubMed) Genome Biol. 19:15 (2018)

Registry entries: Bioconda

python3-cgecore

??? missing short description for package python3-cgecore :-(

https://bitbucket.org/genomicepidemiology/cge_core_module/

Maintainer: Debian Med Packaging Team (Alexandre Detiste)

Versions of package python3-cgecore
Release	Version	Architectures
bullseye	1.5.6+ds-1	all
trixie	1.5.6+ds-2	all
forky	1.5.6+ds-2	all
sid	1.5.6+ds-2	all
bookworm	1.5.6+ds-1	all
upstream	2.0.1

Popcon: 4 users (35 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

python3-cyvcf2

??? missing short description for package python3-cyvcf2 :-(

https://github.com/brentp/cyvcf2

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package python3-cyvcf2
Release	Version	Architectures
sid	0.32.0-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	0.30.18-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	0.30.4-4	amd64,arm64,armhf,i386
trixie	0.31.1-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	0.32.0-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
upstream	0.32.1

Popcon: 9 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Brent S. Pedersen and Aaron R. Quinlan: cyvcf2: fast, flexible variant analysis with Python. (eprint) Bioinformatics 33(12):1867–1869 (2017)

Registry entries: Bio.tools Bioconda

python3-deeptools

??? missing short description for package python3-deeptools :-(

https://github.com/deeptools/deepTools

Maintainer: Debian Med Packaging Team (Alexandre Detiste)

Versions of package python3-deeptools
Release	Version	Architectures
forky	3.5.6+dfsg-1	all
sid	3.5.6+dfsg-1	all
bullseye	3.5.0-1	all
bookworm	3.5.1-3	all
trixie	3.5.6+dfsg-1	all

Popcon: 11 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Fidel Ramirez, Devon P. Ryan, Björn Grüning, Sarah Diehl, Vivek Bhardwaj, Fabian Kilpert, Andreas S Richter, Steffen Heyne, Friederike Dündar and Thomas Manke: deepTools2: a next generation web server for deep-sequencing data analysis. (eprint) Nucleic Acids Research :W160–W165 (2016)

Registry entries: Bio.tools Bioconda

python3-deeptoolsintervals

??? missing short description for package python3-deeptoolsintervals :-(

https://github.com/deeptools/deeptools_intervals/

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package python3-deeptoolsintervals
Release	Version	Architectures
forky	0.1.9-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	0.1.9-3	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye	0.1.9-3	amd64,arm64,armhf,i386
bookworm	0.1.9-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	0.1.9-3	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

Popcon: 11 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

python3-htseq

??? missing short description for package python3-htseq :-(

https://www-huber.embl.de/users/anders/HTSeq/doc/overview.html

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package python3-htseq
Release	Version	Architectures
trixie	2.0.9+dfsg-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64
bookworm	1.99.2-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el
sid	2.0.9+dfsg-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
bullseye	0.13.5-1	amd64,arm64,armhf,i386
forky	2.0.9+dfsg-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
upstream	2.1.2

Popcon: 27 users (35 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

Please cite: Simon Anders, Paul Theodor Pyl and Wolfgang Huber: HTSeq—a Python framework to work with high-throughput sequencing data. (PubMed,eprint) Bioinformatics 31(2):166-169 (2015)

Registry entries: Bio.tools SciCrunch Bioconda

python3-intake

??? missing short description for package python3-intake :-(

https://github.com/intake/intake

Maintainer: Debian Med Packaging Team (Andreas Tille)

Popcon: 1 users (0 upd.)^*

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License: DFSG free

Official Debian package

Git

python3-loompy

??? missing short description for package python3-loompy :-(

https://github.com/linnarsson-lab/loompy

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package python3-loompy
Release	Version	Architectures
bookworm	3.0.7+dfsg-2	amd64,arm64,mips64el,ppc64el,s390x
trixie	3.0.7+dfsg-4	amd64,arm64
forky	3.0.8+dfsg-1	amd64,arm64,ppc64el
sid	3.0.8+dfsg-1	amd64,arm64,ppc64el

Popcon: 0 users (2 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

python3-nanoget

??? missing short description for package python3-nanoget :-(

https://github.com/wdecoster/nanoget

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package python3-nanoget
Release	Version	Architectures
trixie	1.19.3-1	all
bookworm	1.16.1-2	all
bullseye	1.12.2-4	all
sid	1.19.3-1	all
forky	1.19.3-1	all
upstream	1.46.2

Popcon: 3 users (35 upd.)^*

Newer upstream!

License: DFSG free

Official Debian package

Git

The package is enhanced by the following packages: python3-nanoget-examples

python3-nanomath

??? missing short description for package python3-nanomath :-(

https://github.com/wdecoster/nanomath

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package python3-nanomath
Release	Version	Architectures
trixie	1.2.1+ds-1	all
bookworm	1.2.1+ds-1	all
sid	1.4.0+ds-1	all
forky	1.4.0+ds-1	all
bullseye	1.2.0+ds-1	all

Popcon: 8 users (33 upd.)^*

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License: DFSG free

Official Debian package

Git

python3-ncls

??? missing short description for package python3-ncls :-(

https://github.com/biocore-ntnu/ncls

Maintainer: Debian Python Team (Colin Watson)

Versions of package python3-ncls
Release	Version	Architectures
trixie	0.0.63-hotfix+ds-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	0.0.57+ds-1	amd64,arm64,armhf,i386
sid	0.0.70+ds-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky	0.0.70+ds-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm	0.0.63-hotfix+ds-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

Popcon: 2 users (35 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Endre Bakken Stovner and Pål Sætrom: PyRanges: efficient comparison of genomic intervals in Python. Bioinformatics 36(3):918–919 (2020)

python3-py2bit

??? missing short description for package python3-py2bit :-(

https://github.com/deeptools/py2bit/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package python3-py2bit
Release	Version	Architectures
bullseye	0.3.0-6	amd64,arm64,armhf,i386
bookworm	0.3.1-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el
trixie	0.3.3-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64
forky	0.3.3-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
sid	0.3.3-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
upstream	1.0.1

Popcon: 12 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

python3-pybel

??? missing short description for package python3-pybel :-(

https://pybel.readthedocs.io

Maintainer: Debian Med Packaging Team (Aryan Karamtoth)

Versions of package python3-pybel
Release	Version	Architectures
forky	0.15.5-4	all
sid	0.15.5-4	all
bullseye	0.14.10-1	all
bookworm	0.14.10-1	all
trixie	0.15.5-1	all

Popcon: 9 users (33 upd.)^*

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Official Debian package

Git

Please cite: Charles Tapley Hoyt, Andrej Konotopez and Christian Ebeling: PyBEL: a computational framework for Biological Expression Language. (eprint) Bioinformatics 34(4):703–704 (2018)

Registry entries: Bio.tools Bioconda

python3-pychopper

??? missing short description for package python3-pychopper :-(

https://github.com/epi2me-labs/pychopper

Maintainer: Debian Med Packaging Team (Karsten Schöke)

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License: DFSG free

Official Debian package

Git

Registry entries: Bioconda

python3-pyfaidx

??? missing short description for package python3-pyfaidx :-(

https://github.com/mdshw5/pyfaidx

Maintainer: Debian Med Packaging Team (Alexandre Detiste)

Versions of package python3-pyfaidx
Release	Version	Architectures
sid	0.8.1.3-2	all
bullseye	0.5.9.2-1	all
bookworm	0.7.1-2	all
forky	0.8.1.3-2	all
trixie	0.8.1.3-2	all
upstream	0.9.0.4

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Please cite: Matthew D. Shirley, Zhaorong Ma, Brent S. Pedersen and Sarah J. Wheelan: Efficient "pythonic" access to FASTA files using pyfaidx. PeerJ PrePrints 3:e1196 (2015)

Registry entries: Bio.tools

python3-pyflow

??? missing short description for package python3-pyflow :-(

https://illumina.github.io/pyflow/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package python3-pyflow
Release	Version	Architectures
bookworm	1.1.20-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.1.20-2	amd64,arm64,armhf,i386

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python3-pyranges

??? missing short description for package python3-pyranges :-(

https://github.com/biocore-ntnu/pyranges

Maintainer: Debian Med Packaging Team (Aryan Karamtoth)

Versions of package python3-pyranges
Release	Version	Architectures
bullseye	0.0.85+ds-1	all
trixie	0.0.111+ds-9	all
forky	0.0.111+ds-11	all
sid	0.0.111+ds-11	all
bookworm	0.0.111+ds-4	all
upstream	0.1.5

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Official Debian package

Git

Please cite: Endre Bakken Stovner and Pål Sætrom: PyRanges: efficient comparison of genomic intervals in Python. Bioinformatics 36(3):918–919 (2020)

Registry entries: Bio.tools Bioconda

python3-pyrle

??? missing short description for package python3-pyrle :-(

https://github.com/pyranges/pyrle

Maintainer: Debian Python Team (Pieter Lenaerts)

Versions of package python3-pyrle
Release	Version	Architectures
bookworm	0.0.33-4	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	0.0.31-2	amd64,arm64,armhf,i386
trixie	0.0.33-4.1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	0.0.33-5	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
sid	0.0.43-1	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64

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python3-pysam

??? missing short description for package python3-pysam :-(

https://pysam.readthedocs.org/en/latest

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package python3-pysam
Release	Version	Architectures
sid	0.23.3+ds-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
bullseye	0.15.4+ds-3	amd64,arm64,armhf,i386
bookworm	0.20.0+ds-3	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el
trixie	0.23.0+ds-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64
forky	0.23.3+ds-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
upstream	0.24.0

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The package is enhanced by the following packages: python-pysam-tests

Registry entries: Bio.tools Bioconda

python3-tinyalign

??? missing short description for package python3-tinyalign :-(

https://github.com/marcelm/tinyalign

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package python3-tinyalign
Release	Version	Architectures
forky	0.2.2-2	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	0.2.2-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	0.2.1-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	0.2-5	amd64,arm64,armhf,i386
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Git

Registry entries: Bioconda

q2-alignment

??? missing short description for package q2-alignment :-(

https://qiime2.org/

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package q2-alignment
Release	Version	Architectures
bullseye	2020.11.1-2	all
bookworm	2022.11.1-2	all
sid	2024.5.0-1	all
upstream	2026.4.0

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Git

q2-cutadapt

??? missing short description for package q2-cutadapt :-(

https://qiime2.org/

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package q2-cutadapt
Release	Version	Architectures
sid	2024.5.0-1	amd64,arm64,loong64,ppc64el,riscv64
bullseye	2020.11.1-1	amd64,arm64
bookworm	2022.11.1-2	amd64,arm64,mips64el,ppc64el
upstream	2026.4.0

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Git

q2-dada2

??? missing short description for package q2-dada2 :-(

https://qiime2.org/

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package q2-dada2
Release	Version	Architectures
bookworm	2022.11.2-2	amd64
bullseye	2020.11.1-3	amd64
sid	2024.5.0-1	amd64
upstream	2026.4.0

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q2-demux

??? missing short description for package q2-demux :-(

https://qiime2.org/

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package q2-demux
Release	Version	Architectures
bullseye	2020.11.1-1	all
bookworm	2022.11.1+dfsg-2	all
sid	2024.5.0+dfsg-1	all
upstream	2026.4.0

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Git

q2-emperor

??? missing short description for package q2-emperor :-(

https://qiime2.org/

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

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q2-feature-classifier

??? missing short description for package q2-feature-classifier :-(

https://qiime2.org/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package q2-feature-classifier
Release	Version	Architectures
sid	2024.5.0-1	all
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bookworm	2022.11.1-2	all
upstream	2026.4.0

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Official Debian package

Git

Registry entries: Bio.tools

q2-feature-table

??? missing short description for package q2-feature-table :-(

https://qiime2.org/

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package q2-feature-table
Release	Version	Architectures
bullseye	2020.11.1+dfsg-1	all
sid	2024.5.0+dfsg-1	all
bookworm	2022.11.1+dfsg-2	all
upstream	2026.4.0

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q2-fragment-insertion

??? missing short description for package q2-fragment-insertion :-(

https://qiime2.org/

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package q2-fragment-insertion
Release	Version	Architectures
sid	2024.5.0-1	amd64,arm64,loong64,ppc64el,riscv64
bookworm	2022.11.1-3	amd64,arm64,mips64el,ppc64el
upstream	2026.4.0

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Git

q2-metadata

??? missing short description for package q2-metadata :-(

https://qiime2.org/

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package q2-metadata
Release	Version	Architectures
sid	2024.5.0+dfsg-1	amd64,arm64,loong64,ppc64el,riscv64
bullseye	2020.11.1+dfsg-1	amd64,arm64
bookworm	2022.8.0-1	amd64,arm64,mips64el,ppc64el
upstream	2026.4.0

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Official Debian package

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q2-phylogeny

??? missing short description for package q2-phylogeny :-(

https://qiime2.org/

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package q2-phylogeny
Release	Version	Architectures
sid	2024.5.0-1	amd64
bookworm	2022.11.1-3	amd64
experimental	2022.11.1-1	all
upstream	2026.4.0

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Git

q2-quality-control

??? missing short description for package q2-quality-control :-(

https://qiime2.org/

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package q2-quality-control
Release	Version	Architectures
sid	2024.5.0-2	all
bullseye	2020.11.1-3	all
bookworm	2022.11.1-2	all
upstream	2026.4.0

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Official Debian package

Git

q2-quality-filter

??? missing short description for package q2-quality-filter :-(

https://qiime2.org/

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package q2-quality-filter
Release	Version	Architectures
bookworm	2022.11.1-2	all
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sid	2024.5.0-1	all
upstream	2026.4.0

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Git

q2-sample-classifier

??? missing short description for package q2-sample-classifier :-(

https://qiime2.org

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package q2-sample-classifier
Release	Version	Architectures
bookworm	2022.11.1-3	all
sid	2024.5.0-2	all
bullseye	2020.11.1-3	all
upstream	2026.4.0

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Official Debian package

Git

Registry entries: Bio.tools

q2-taxa

??? missing short description for package q2-taxa :-(

https://qiime2.org/

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package q2-taxa
Release	Version	Architectures
sid	2024.5.0+dfsg-1	all
bullseye	2020.11.1+dfsg-2	all
bookworm	2022.11.1+dfsg-2	all
upstream	2026.4.0

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Git

q2-types

??? missing short description for package q2-types :-(

https://qiime2.org/

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package q2-types
Release	Version	Architectures
bullseye	2020.11.1-1	all
bookworm	2022.11.1-2	all
sid	2024.5.0-1	all
upstream	2026.4.0

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Official Debian package

Git

q2cli

??? missing short description for package q2cli :-(

https://qiime2.org/

Maintainer: Debian Med Packaging Team (Michael R. Crusoe)

Versions of package q2cli
Release	Version	Architectures
sid	2024.5.0-2	all
bookworm	2022.11.1-2	all
bullseye	2020.11.1-1	all
upstream	2026.4.0

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Official Debian package

Git

q2templates

??? missing short description for package q2templates :-(

https://qiime2.org/

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package q2templates
Release	Version	Architectures
sid	2024.5.0+ds-4	all
forky	2024.5.0+ds-4	all
trixie	2024.5.0+ds-3	all
bookworm	2022.11.1+ds-2	all
bullseye	2020.11.1+dfsg-1	all
upstream	2026.4.0

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Official Debian package

Git

r-bioc-annotationhub

??? missing short description for package r-bioc-annotationhub :-(

https://bioconductor.org/packages/AnnotationHub/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-annotationhub
Release	Version	Architectures
trixie	3.14.0+dfsg-2	all
bookworm	3.6.0+dfsg-1	all
bullseye	2.22.0+dfsg-1	all
sid	3.14.0+dfsg-3	all
upstream	4.2.0

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Official Debian package

Git

Registry entries: Bio.tools

r-bioc-aroma.light

??? missing short description for package r-bioc-aroma.light :-(

https://bioconductor.org/packages/aroma.light/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-aroma.light
Release	Version	Architectures
sid	3.36.0-3	all
bullseye	3.20.0-1	all
bookworm	3.28.0-1	all
trixie	3.36.0-2	all
upstream	3.42.0

Popcon: 8 users (34 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Henrik Bengtsson, Pierre Neuvial and Terence P. Speed: TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays. (PubMed,eprint) BMC Bioinformatics 11:245 (2010)

Registry entries: Bio.tools SciCrunch Bioconda

r-bioc-beachmat

??? missing short description for package r-bioc-beachmat :-(

https://bioconductor.org/packages/beachmat/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-beachmat
Release	Version	Architectures
bullseye	2.6.4+ds-1	amd64,arm64,armhf,i386
trixie	2.22.0+ds-3~deb13u1	amd64,arm64,ppc64el,riscv64,s390x
bookworm	2.14.0+ds-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	2.22.0+ds-4	amd64,arm64,loong64,ppc64el,riscv64
upstream	2.28.0

Popcon: 8 users (37 upd.)^*

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License: DFSG free

Official Debian package

Git

r-bioc-biocneighbors

??? missing short description for package r-bioc-biocneighbors :-(

https://bioconductor.org/packages/BiocNeighbors/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-biocneighbors
Release	Version	Architectures
trixie	2.0.1+ds-2	amd64,arm64,ppc64el,riscv64,s390x
bookworm	1.16.0+ds-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	2.0.1+ds-3	amd64,arm64,loong64,ppc64el,riscv64
bullseye	1.8.2+ds-1	amd64,arm64,armhf,i386
upstream	2.6.0

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Official Debian package

Git

r-bioc-biocsingular

??? missing short description for package r-bioc-biocsingular :-(

https://bioconductor.org/packages/BiocSingular/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-biocsingular
Release	Version	Architectures
bullseye	1.6.0+ds-1	amd64,arm64,armhf,i386
trixie	1.22.0+ds-2	amd64,arm64,ppc64el,riscv64,s390x
bookworm	1.14.0+ds-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	1.22.0+ds-3	amd64,arm64,loong64,ppc64el,riscv64
upstream	1.28.0

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Official Debian package

Git

r-bioc-ctc

??? missing short description for package r-bioc-ctc :-(

https://bioconductor.org/packages/ctc/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-ctc
Release	Version	Architectures
bullseye	1.64.0-1	all
sid	1.80.0-3	all
bookworm	1.72.0-1	all
trixie	1.80.0-2	all
upstream	1.86.0

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Official Debian package

Git

Registry entries: Bioconda

r-bioc-dnacopy

??? missing short description for package r-bioc-dnacopy :-(

https://www.bioconductor.org/packages/DNAcopy/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-dnacopy
Release	Version	Architectures
trixie	1.80.0-2	amd64,arm64,ppc64el,riscv64,s390x
sid	1.80.0-3	amd64,arm64,loong64,ppc64el,riscv64
bookworm	1.72.3-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.64.0-1	amd64,arm64,armhf,i386
upstream	1.86.0

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Official Debian package

Git

Registry entries: Bio.tools SciCrunch Bioconda

r-bioc-ensembldb

??? missing short description for package r-bioc-ensembldb :-(

https://bioconductor.org/packages/ensembldb/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-ensembldb
Release	Version	Architectures
trixie	2.30.0+dfsg-3	all
sid	2.30.0+dfsg-4	all
bullseye	2.14.0+dfsg-1	all
bookworm	2.22.0+dfsg-1	all
upstream	2.36.0

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Official Debian package

Git

Registry entries: Bio.tools Bioconda

r-bioc-experimenthub

??? missing short description for package r-bioc-experimenthub :-(

https://bioconductor.org/packages/ExperimentHub/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-experimenthub
Release	Version	Architectures
bullseye	1.16.0+ds-1	all
sid	2.14.0+ds-3	all
bookworm	2.6.0+ds-1	all
trixie	2.14.0+ds-2	all
upstream	3.2.0

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Official Debian package

Git

r-bioc-geneplotter

??? missing short description for package r-bioc-geneplotter :-(

https://bioconductor.org/packages/geneplotter/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-geneplotter
Release	Version	Architectures
sid	1.84.0+dfsg-3	all
trixie	1.84.0+dfsg-2	all
bookworm	1.76.0-1	all
bullseye	1.68.0-1	all
upstream	1.90.0

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Official Debian package

Git

Registry entries: Bio.tools Bioconda

r-bioc-genomicalignments

??? missing short description for package r-bioc-genomicalignments :-(

https://bioconductor.org/packages/GenomicAlignments/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-genomicalignments
Release	Version	Architectures
bullseye	1.26.0-1	amd64,arm64,armhf,i386
trixie	1.42.0-2	amd64,arm64,ppc64el,riscv64,s390x
sid	1.42.0-3	amd64,arm64,loong64,ppc64el,riscv64
bookworm	1.34.0-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream	1.48.0

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Official Debian package

Git

Please cite: Michael Lawrence, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin T. Morgan and Vincent J. Carey: Software for Computing and Annotating Genomic Ranges. (PubMed,eprint) PLoS Computational Biology 9(8):e1003118 (2013)

Registry entries: Bio.tools Bioconda

r-bioc-genomicfiles

??? missing short description for package r-bioc-genomicfiles :-(

https://bioconductor.org/packages/GenomicFiles/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-genomicfiles
Release	Version	Architectures
sid	1.42.0+dfsg-3	all
trixie	1.42.0+dfsg-2	all
bookworm	1.34.0-1	all
bullseye	1.26.0-1	all
upstream	1.48.0

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Official Debian package

Git

Registry entries: Bio.tools Bioconda

r-bioc-genomicranges

??? missing short description for package r-bioc-genomicranges :-(

https://bioconductor.org/packages/GenomicRanges/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-genomicranges
Release	Version	Architectures
sid	1.58.0+dfsg-3	amd64,arm64,loong64,ppc64el,riscv64
trixie	1.58.0+dfsg-2	amd64,arm64,ppc64el,riscv64,s390x
bookworm	1.50.2+dfsg-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.42.0+dfsg-1	amd64,arm64,armhf,i386
upstream	1.64.0

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Official Debian package

Git

Registry entries: Bio.tools SciCrunch Bioconda

r-bioc-go.db

??? missing short description for package r-bioc-go.db :-(

https://bioconductor.org/packages/GO.db/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-go.db
Release	Version	Architectures
bullseye	3.12.1-1	all
trixie	3.20.0-2	all
bookworm	3.16.0-1	all
sid	3.20.0-3	all
upstream	3.23.1

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Official Debian package

Git

Registry entries: Bioconda

r-bioc-grohmm

??? missing short description for package r-bioc-grohmm :-(

https://bioconductor.org/packages/groHMM/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-grohmm
Release	Version	Architectures
bookworm	1.32.0-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye	1.24.0-1	amd64,arm64,armhf,i386
sid	1.40.3-4	amd64,arm64,loong64,ppc64el,riscv64
trixie	1.40.3-3	amd64,arm64,ppc64el,riscv64,s390x
upstream	1.46.0

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License: DFSG free

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Git

Please cite: Minho Chae, Charles G. Danko and and W. Lee Kraus: groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data. (PubMed) BMC Bioinformatics 16:222.0 (2015)

Registry entries: Bio.tools Bioconda

r-bioc-gviz

??? missing short description for package r-bioc-gviz :-(

https://bioconductor.org/packages/Gviz/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-gviz
Release	Version	Architectures
bookworm	1.42.1+dfsg-1	all
trixie	1.50.0+dfsg-2	all
sid	1.50.0+dfsg-3	all
bullseye	1.34.0+dfsg-1	all
upstream	1.56.0

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Please cite: Michael Lawrence, Robert Gentleman and "Vincent Carey: rtracklayer: an R package for interfacing with genome browsers. (PubMed,eprint) Bioinformatics 25(14):1841-1842 (2009)

Registry entries: Bio.tools Bioconda

r-bioc-isoformswitchanalyzer

??? missing short description for package r-bioc-isoformswitchanalyzer :-(

https://bioconductor.org/packages/IsoformSwitchAnalyzeR/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-isoformswitchanalyzer
Release	Version	Architectures
sid	2.6.0+ds-3	amd64,arm64,loong64,ppc64el,riscv64
bookworm	1.20.0+ds-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	2.6.0+ds-2	amd64,arm64,ppc64el,riscv64,s390x
upstream	2.12.0

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Official Debian package

Git

Registry entries: Bio.tools Bioconda

r-bioc-org.hs.eg.db

??? missing short description for package r-bioc-org.hs.eg.db :-(

https://bioconductor.org/packages/org.Hs.eg.db/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-org.hs.eg.db
Release	Version	Architectures
sid	3.20.0-4	all
trixie	3.20.0-3	all
bookworm	3.16.0-1	all
bullseye	3.12.0-1	all
upstream	3.23.1

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Git

Registry entries: Bioconda

r-bioc-qusage

??? missing short description for package r-bioc-qusage :-(

https://bioconductor.org/packages/qusage/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-qusage
Release	Version	Architectures
trixie	2.40.0-2	all
bookworm	2.32.0-1	all
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bullseye	2.24.0-1	all
upstream	2.46.0

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Official Debian package

Git

Please cite: Gur Yaari, Christopher R. Bolen, Juilee Thakar and Steven H. Kleinstein: Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations. (PubMed,eprint) Nucleic Acids Res. 41(18):e170 (2013)

Registry entries: Bioconda

r-bioc-savr

??? missing short description for package r-bioc-savr :-(

https://bioconductor.org/packages/savR/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

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Official Debian package

Git

Registry entries: Bio.tools Bioconda

r-bioc-singlecellexperiment

??? missing short description for package r-bioc-singlecellexperiment :-(

https://bioconductor.org/packages/SingleCellExperiment/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-singlecellexperiment
Release	Version	Architectures
bullseye	1.12.0+ds-1	all
bookworm	1.20.0+ds-1	all
trixie	1.28.1+ds-2	all
sid	1.28.1+ds-3	all
upstream	1.34.0

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r-bioc-structuralvariantannotation

??? missing short description for package r-bioc-structuralvariantannotation :-(

https://bioconductor.org/packages/StructuralVariantAnnotation/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-structuralvariantannotation
Release	Version	Architectures
sid	1.22.0+ds-3	all
bookworm	1.13.0+ds-1	all
trixie	1.22.0+ds-2	all
upstream	1.28.0

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License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools Bioconda

r-bioc-tximport

??? missing short description for package r-bioc-tximport :-(

https://bioconductor.org/packages/tximport/

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-bioc-tximport
Release	Version	Architectures
trixie	1.34.0+dfsg-2	all
bookworm	1.26.1+dfsg-1	all
bullseye	1.18.0+dfsg-1	all
sid	1.34.0+dfsg-3	all
upstream	1.40.0

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Git

Please cite: Charlotte Soneson, Michael I. Love and Mark D. Robinson: Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000Research 4:1521 (2015)

Registry entries: Bio.tools Bioconda

r-cran-amap

??? missing short description for package r-cran-amap :-(

https://cran.r-project.org/package=amap

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-amap
Release	Version	Architectures
bullseye	0.8-18-2	amd64,arm64,armhf,i386
sid	0.8-20-3	amd64,arm64,loong64,ppc64el,riscv64
sid	0.8-20-2	armhf,i386,s390x
forky	0.8-20-2	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
trixie	0.8-20-2	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	0.8-19-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

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Official Debian package

Git

r-cran-biwt

??? missing short description for package r-cran-biwt :-(

https://cran.r-project.org/package=biwt

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-biwt
Release	Version	Architectures
forky	1.0.1-3	all
bullseye	1.0-2	amd64,arm64,armhf,i386
sid	1.0.1-3	all
trixie	1.0.1-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.0.1-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

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License: DFSG free

Official Debian package

Git

r-cran-boolnet

??? missing short description for package r-cran-boolnet :-(

https://cran.r-project.org/package=BoolNet

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-boolnet
Release	Version	Architectures
sid	2.1.9-2	amd64,arm64,loong64,ppc64el,riscv64
bullseye	2.1.5-3	amd64,arm64,armhf,i386
bookworm	2.1.7-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	2.1.9-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	2.1.9-1	armhf,i386,s390x

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License: DFSG free

Official Debian package

Git

Please cite: Christoph Muessel, Martin Hopfensitz and Hans A. Kestler: BoolNet -- an R package for generation, reconstruction and analysis of Boolean networks. (eprint) Bioinformatics 26(6):1378-1380 (2010)

r-cran-corrplot

??? missing short description for package r-cran-corrplot :-(

https://cran.r-project.org/package=corrplot

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-corrplot
Release	Version	Architectures
bookworm	0.92-1	all
sid	0.95-2	all
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trixie	0.95-1	all
bullseye	0.84-3	all

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Official Debian package

Git

r-cran-dynamictreecut

??? missing short description for package r-cran-dynamictreecut :-(

https://cran.r-project.org/package=dynamicTreeCut

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-dynamictreecut
Release	Version	Architectures
trixie	1.63-1-3	all
bullseye	1.63-1-3	all
sid	1.63-1-4	all
forky	1.63-1-4	all
bookworm	1.63-1-3	all

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License: DFSG free

Official Debian package

Git

r-cran-epir

??? missing short description for package r-cran-epir :-(

https://cran.r-project.org/package=epiR

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Popcon: 136 users (134 upd.)^*

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License: DFSG free

Official Debian package

Git

r-cran-fitdistrplus

??? missing short description for package r-cran-fitdistrplus :-(

https://cran.r-project.org/package=fitdistrplus

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-fitdistrplus
Release	Version	Architectures
trixie	1.2-2-1	all
bullseye	1.1-3-1	all
forky	1.2-6-1	all
sid	1.2-6-1	all
bookworm	1.1-8-1	all

Popcon: 7 users (39 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Marie Laure Delignette-Muller Christophe Dutang: fitdistrplus: An R Package for Fitting Distributions. Journal of Statistical Software 64(4):1-34 (2015)

r-cran-forecast

??? missing short description for package r-cran-forecast :-(

https://cran.r-project.org/package=forecast

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-forecast
Release	Version	Architectures
sid	9.0.2-1	amd64,arm64,loong64,ppc64el,riscv64
bullseye	8.13-1	amd64,arm64,armhf,i386
bookworm	8.20-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	8.23.0-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

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License: DFSG free

Official Debian package

Git

r-cran-gprofiler2

??? missing short description for package r-cran-gprofiler2 :-(

https://cran.r-project.org/package=gprofiler2

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Popcon: 4 users (36 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools SciCrunch

r-cran-minerva

??? missing short description for package r-cran-minerva :-(

https://cran.r-project.org/package=minerva

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-minerva
Release	Version	Architectures
sid	1.5.10-2	amd64,arm64,loong64,ppc64el,riscv64
forky	1.5.10-1	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
trixie	1.5.10-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye	1.5.8-2	amd64,arm64,armhf,i386
sid	1.5.10-1	armhf,i386,s390x
bookworm	1.5.10-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

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License: DFSG free

Official Debian package

Git

r-cran-optimalcutpoints

??? missing short description for package r-cran-optimalcutpoints :-(

https://cran.r-project.org/package=OptimalCutpoints

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-optimalcutpoints
Release	Version	Architectures
sid	1.1-5-2	all
forky	1.1-5-2	all
bookworm	1.1-5-1	all
bullseye	1.1-4-2	all
trixie	1.1-5-1	all

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License: DFSG free

Official Debian package

Git

Please cite: Mónica López-Ratón María Xosé Rodríguez-Álvarez, Carmen Cadarso Suárez and Francisco Gude Sampedro: OptimalCutpoints: An R Package for Selecting Optimal Cutpoints in Diagnostic Tests. Journal of Statistical Software 61(8):1-36 (2014)

r-cran-parmigene

??? missing short description for package r-cran-parmigene :-(

https://cran.r-project.org/package=parmigene

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-parmigene
Release	Version	Architectures
sid	1.1.1-2	amd64,arm64,loong64,ppc64el,riscv64
bullseye	1.1.0-1	amd64,arm64,armhf,i386
bookworm	1.1.0-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	1.1.1-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	1.1.1-1	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
sid	1.1.1-1	armhf,i386,s390x

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License: DFSG free

Official Debian package

Git

r-cran-pheatmap

??? missing short description for package r-cran-pheatmap :-(

https://cran.r-project.org/package=pheatmap

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-pheatmap
Release	Version	Architectures
bookworm	1.0.12-2	all
bullseye	1.0.12-2	all
sid	1.0.13-1	all
forky	1.0.13-1	all
trixie	1.0.12-2	all

Popcon: 37 users (39 upd.)^*

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License: DFSG free

Official Debian package

Git

Registry entries: Bio.tools

r-cran-qqman

??? missing short description for package r-cran-qqman :-(

https://cran.r-project.org/package=qqman

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-qqman
Release	Version	Architectures
forky	0.1.9+dfsg-2	all
bookworm	0.1.8+dfsg-1	all
sid	0.1.9+dfsg-2	all
trixie	0.1.9+dfsg-1	all
bullseye	0.1.4-7	all

Popcon: 1 users (36 upd.)^*

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License: DFSG free

Official Debian package

Git

Please cite: Stephen D. Turner: qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. (eprint) bioRxiv (2014)

r-cran-rcpphnsw

??? missing short description for package r-cran-rcpphnsw :-(

https://cran.r-project.org/package=RcppHNSW

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-rcpphnsw
Release	Version	Architectures
bullseye	0.3.0.9001+ds-1	amd64,arm64,armhf,i386
bookworm	0.4.1+ds-2	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	0.6.0+ds-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky	0.6.0+ds-1	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
sid	0.6.0+ds-1	armhf,i386,s390x
sid	0.6.0+ds-2	amd64,arm64,loong64,ppc64el,riscv64

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Official Debian package

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r-cran-rentrez

??? missing short description for package r-cran-rentrez :-(

https://cran.r-project.org/package=rentrez

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-rentrez
Release	Version	Architectures
forky	1.2.4+dfsg-1	all
sid	1.2.4+dfsg-1	all
bullseye	1.2.3+dfsg-1	all
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trixie	1.2.3+dfsg-1	all

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Official Debian package

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r-cran-sctransform

??? missing short description for package r-cran-sctransform :-(

https://cran.r-project.org/package=sctransform

Maintainer: Debian R Packages Maintainers (Charles Plessy)

Versions of package r-cran-sctransform
Release	Version	Architectures
bullseye	0.3.2-1	amd64,arm64,armhf,i386
trixie	0.4.1-1	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid	0.4.3-1	amd64,arm64,loong64,ppc64el,riscv64
bookworm	0.3.5-1	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid	0.4.1-1	armhf,i386,s390x

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License: DFSG free

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Registry entries: Bio.tools

resfinder-db

??? missing short description for package resfinder-db :-(

https://bitbucket.org/genomicepidemiology/resfinder

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package resfinder-db
Release	Version	Architectures
bookworm	0.0+git20220524.fa32d9a-1	all
sid	0.0+git20220524.fa32d9a-2	all
trixie	0.0+git20220524.fa32d9a-1	all
forky	0.0+git20220524.fa32d9a-2	all
bullseye	0.0+git20200408.0322c0d-1	all
upstream	0.0+git20260126.eecf0aa

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Git

science-workflow

??? missing short description for package science-workflow :-(

https://wiki.debian.org/DebianScience/

Maintainer: Debian Science Team (Andreas Tille)

Popcon: 20 users (100 upd.)^*

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Debian packages in contrib or non-free

arb

??? missing short description for package arb :-(

http://www.arb-home.de/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package arb
Release	Version	Architectures
trixie	6.0.6-8 (non-free)	amd64,arm64,armel,armhf,i386,riscv64,s390x
bookworm	6.0.6-5 (non-free)	amd64,i386
bullseye	6.0.6-4 (non-free)	amd64,i386
sid	6.0.6-8 (non-free)	amd64,arm64,armhf,i386,riscv64,s390x
upstream	7.0

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License: non-free

Debian package in contrib/non-free

Git

blimps-utils

??? missing short description for package blimps-utils :-(

https://web.archive.org/web/20170606235903/http://blocks.fhcrc.org/blocks/uploads/blimps/

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package blimps-utils
Release	Version	Architectures
bookworm	3.9+ds-1 (non-free)	amd64
bullseye	3.9+ds-1 (non-free)	amd64
sid	3.9+ds-4 (non-free)	amd64
trixie	3.9+ds-4 (non-free)	amd64

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License: non-free

Debian package in contrib/non-free

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The package is enhanced by the following packages: blimps-examples

Please cite: J. G. Henikoff, S. Pietrokovski, C. M. McCallum and S. Henikoff: Blocks-based methods for detecting protein homology. (PubMed,eprint) Electrophoresis 21(9):1700-6 (2000)

caftools

??? missing short description for package caftools :-(

https://www.sanger.ac.uk/science/tools/caf

Maintainer: Steffen Moeller

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License: non-free

Debian package in contrib/non-free

Git

Please cite: Simon Dear, Richard Durbin, LaDeana Hillier, Gabor Marth, Jean Thierry-Mieg and and Richard Mott: Sequence assembly with CAFTOOLS. (PubMed,eprint) Genome research 8(3):260-267 (1998)

Registry entries: Bio.tools

cluster3

??? missing short description for package cluster3 :-(

http://bonsai.hgc.jp/~mdehoon/software/cluster/

Maintainer: Debian Med Packaging Team (tony mancill)

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License: non-free

Debian package in contrib/non-free

Git

Please cite: M. J. L. de Hoon, S. Imoto, J. Nolan and S. Miyano: Open Source Clustering Software. (PubMed,eprint) Bioinformatics 20(9):1453-1454 (2004)

cufflinks

??? missing short description for package cufflinks :-(

https://cufflinks.cbcb.umd.edu

Maintainer: Debian Med Packaging Team (Étienne Mollier)

Versions of package cufflinks
Release	Version	Architectures
sid	2.2.1+dfsg.1-10 (non-free)	amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
bullseye	2.2.1+dfsg.1-8 (non-free)	amd64,arm64,armhf,i386
bookworm	2.2.1+dfsg.1-9 (non-free)	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie	2.2.1+dfsg.1-10 (non-free)	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x

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License: non-free

Debian package in contrib/non-free

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Please cite: Cole Trapnell, Brian A Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold and Lior Pachter: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. (PubMed) Nature Biotechnology 28(5):511-515 (2010)

Registry entries: Bio.tools SciCrunch Bioconda

relion-cuda

??? missing short description for package relion-cuda :-(

https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package relion-cuda
Release	Version	Architectures
sid	3.1.3-2 (contrib)	amd64
bullseye	3.1.0-2 (contrib)	amd64
bookworm	3.1.3-2 (contrib)	amd64
upstream	5.1.0

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Debian package in contrib/non-free

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relion-gui-cuda

??? missing short description for package relion-gui-cuda :-(

https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package relion-gui-cuda
Release	Version	Architectures
bookworm	3.1.3-2 (contrib)	amd64
bullseye	3.1.0-2 (contrib)	amd64
sid	3.1.3-2 (contrib)	amd64
upstream	5.1.0

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License: DFSG free, but needs non-free components

Debian package in contrib/non-free

Git

seq-gen

??? missing short description for package seq-gen :-(

https://tree.bio.ed.ac.uk/software/seqgen/

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package seq-gen
Release	Version	Architectures
bullseye	1.3.4-2 (non-free)	amd64,arm64,armhf,i386
forky	1.3.5-2 (non-free)	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid	1.3.5-2 (non-free)	amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie	1.3.4-2 (non-free)	amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm	1.3.4-2 (non-free)	amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x

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License: non-free

Debian package in contrib/non-free

Git

Please cite: A. Rambaut and N. C. Grassly: Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. (PubMed,eprint) Comput. Appl. Biosci. 13(3):235-238 (1997)

Registry entries: SciCrunch Bioconda

seqcluster

??? missing short description for package seqcluster :-(

https://github.com/lpantano/seqcluster

Maintainer: Debian Med Packaging Team (Alexandre Detiste)

Versions of package seqcluster
Release	Version	Architectures
trixie	1.2.9+ds-5 (contrib)	all
bookworm	1.2.9+ds-3 (contrib)	all
bullseye	1.2.7+ds-1 (contrib)	all
sid	1.2.9+ds-7 (contrib)	all
forky	1.2.9+ds-7 (contrib)	all

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License: DFSG free, but needs non-free components

Debian package in contrib/non-free

Git

Please cite: Lorena Pantano, Marc R. Friedländer, Georgia Escaramís, Esther Lizano, Joan Pallarès-Albanell, Isidre Ferrer, Xavier Estivill and Eulàlia Martí: Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinson's disease revealed by deep sequencing analysis. (PubMed) Bioinformatics (2015)

Registry entries: Bio.tools

sift

??? missing short description for package sift :-(

https://sift.bii.a-star.edu.sg/

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package sift
Release	Version	Architectures
trixie	6.2.1-1 (non-free)	amd64
bookworm	4.0.3b-6 (non-free)	amd64
bullseye	4.0.3b-6 (non-free)	amd64
sid	6.2.1-2 (non-free)	amd64

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License: non-free

Debian package in contrib/non-free

Git

Please cite: Prateek Kumar, Steven Henikoff and Pauline C Ng: Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. (PubMed,eprint) Nature Protocols 4(7):1073-81 (2009)

Registry entries: Bio.tools SciCrunch

solvate

??? missing short description for package solvate :-(

https://www3.mpibpc.mpg.de/groups/grubmueller/start/index.html

Maintainer: Debian Med Packaging Team (Nilesh Patra)

Versions of package solvate
Release	Version	Architectures
bookworm	1.0-3 (non-free)	amd64
bullseye	1.0-3 (non-free)	amd64
trixie	1.0-3 (non-free)	amd64
sid	1.0-3 (non-free)	amd64
forky	1.0-3 (non-free)	amd64

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License: non-free

Debian package in contrib/non-free

Git

trnascan-se

??? missing short description for package trnascan-se :-(

https://lowelab.ucsc.edu/tRNAscan-SE

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package trnascan-se
Release	Version	Architectures
sid	2.0.12+ds-2 (non-free)	amd64,arm64,i386
bullseye	2.0.7+ds-1 (non-free)	amd64,i386
bookworm	2.0.10+ds-1 (non-free)	amd64,i386
trixie	2.0.12+ds-1 (non-free)	amd64,arm64,i386
forky	2.0.12+ds-2 (non-free)	amd64,arm64,i386

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License: non-free

Debian package in contrib/non-free

Git

Please cite: Todd M Lowe and Sean R Eddy: tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. (PubMed,eprint) Nucleic Acids Research 25(5):955-964 (1997)

Registry entries: Bio.tools SciCrunch Bioconda

varscan

??? missing short description for package varscan :-(

https://dkoboldt.github.io/varscan/

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package varscan
Release	Version	Architectures
bullseye	2.4.3+dfsg-3 (non-free)	amd64
trixie	2.4.3+dfsg-4 (non-free)	amd64
bookworm	2.4.3+dfsg-4 (non-free)	amd64
sid	2.4.3+dfsg-5 (non-free)	amd64
forky	2.4.3+dfsg-5 (non-free)	amd64

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License: non-free

Debian package in contrib/non-free

Git

Please cite: Daniel C. Koboldt, Qunyuan Zhang, David E. Larson, Dong Shen, Michael D. McLellan, Ling Lin, Christopher A. Miller, Elaine R. Mardis, Li Ding and Richard K. Wilson: VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing". (PubMed,eprint) Genome Res. 22(3):568-576 (2012)

Registry entries: Bio.tools SciCrunch Bioconda

vdjtools

??? missing short description for package vdjtools :-(

https://github.com/mikessh/vdjtools

Maintainer: Debian Med Packaging Team (Andreas Tille)

Versions of package vdjtools
Release	Version	Architectures
bullseye	1.2.1+git20190311-5 (non-free)	all
bookworm	1.2.1+git20190311+repack-1 (non-free)	all
trixie	1.2.1+git20190311+repack-2 (non-free)	all
forky	1.2.1+git20190311+repack-2 (non-free)	all
sid	1.2.1+git20190311+repack-2 (non-free)	all

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License: non-free

Debian package in contrib/non-free

Git

Please cite: M Shugay, D.V. Bagaev, M.A. Turchaninova, D.A. Bolotin, O.V. Britanova, E.V. Putintseva, M.V. Pogorelyy, V.I. Nazarov VI, I.V. Zvyagin, V.I. Kirgizova, K.I. Kirgizov, E.V. Skorobogatova and D.M. Chudakov: VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires. (PubMed,eprint) PLoS Comput Biol. 11(11):e1004503 (2015)

vienna-rna

??? missing short description for package vienna-rna :-(

https://www.tbi.univie.ac.at/RNA/

Maintainer: Debian Med Packaging Team (Santiago Vila)

Versions of package vienna-rna
Release	Version	Architectures
bullseye	2.4.17+dfsg-2 (non-free)	amd64,arm64,armhf
trixie	2.6.4+dfsg-1 (non-free)	amd64,arm64,armel,armhf,ppc64el,riscv64,s390x
bookworm	2.5.1+dfsg-1 (non-free)	amd64,arm64,mips64el,ppc64el,s390x
sid	2.7.0+dfsg-2 (non-free)	amd64,arm64,armhf,loong64,ppc64el,riscv64,s390x
forky	2.7.0+dfsg-2 (non-free)	amd64,arm64,armhf,ppc64el,riscv64,s390x
upstream	2.7.2

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