Debian Med Project
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Summary
Phylogeny
Debian Med phylogeny packages

This lists Debian packages related to phylogeny for use in life sciences. The purpose of this compilation of packages is to have a handy subset of from the med-bio metapackage which contains a lot more than only phylogeny related software.

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Description

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for Debian Med to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the Debian Med mailing list

Links to other tasks
Index of all tasks

Debian Med Phylogeny packages

Official Debian packages with high relevance

altree
??? missing short description for package altree :-(
Versions of package altree
ReleaseVersionArchitectures
bullseye1.3.1-10amd64,arm64,armhf,i386
bookworm1.3.2-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky1.3.2-4amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid1.3.2-4amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie1.3.2-2amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
Debtags of package altree:
fieldbiology, biology:bioinformatics
interfacecommandline
roleprogram, shared-lib
scopeutility
useanalysing, comparing
works-with-formatplaintext
Popcon: 7 users (32 upd.)*
Versions and Archs
 License: DFSG free
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 
beast-mcmc
??? missing short description for package beast-mcmc :-(
Versions of package beast-mcmc
ReleaseVersionArchitectures
bullseye1.10.4+dfsg-2all
bookworm1.10.4+dfsg-5all
trixie1.10.4+dfsg-7all
sid1.10.4+dfsg-8all
upstream10.5.0
Popcon: 6 users (33 upd.)*
Newer upstream!
 License: DFSG free
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 
clustalw
??? missing short description for package clustalw :-(
Versions of package clustalw
ReleaseVersionArchitectures
sid2.1+lgpl-7amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye2.1+lgpl-7amd64,arm64,armhf,i386
bookworm2.1+lgpl-7amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie2.1+lgpl-7amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky2.1+lgpl-7amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
Debtags of package clustalw:
biologyformat:aln, nuceleic-acids, peptidic
fieldbiology, biology:bioinformatics
interfacecommandline, text-mode
roleprogram
scopeutility
usecomparing
works-with-formatplaintext
Popcon: 17 users (37 upd.)*
Versions and Archs
 License: DFSG free
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 :-(
Versions of package clustalx
ReleaseVersionArchitectures
trixie2.1+lgpl-9amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm2.1+lgpl-9amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye2.1+lgpl-9amd64,arm64,armhf,i386
sid2.1+lgpl-9amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky2.1+lgpl-9amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
Debtags of package clustalx:
biologyformat:aln, nuceleic-acids, peptidic
fieldbiology, biology:bioinformatics
interfacex11
roleprogram
scopeutility
uitoolkitmotif
useanalysing, comparing, viewing
works-with-formatplaintext
x11application
Popcon: 11 users (36 upd.)*
Versions and Archs
 License: DFSG free
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
dialign
??? missing short description for package dialign :-(
Versions of package dialign
ReleaseVersionArchitectures
forky2.2.1-13amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid2.2.1-13amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie2.2.1-13amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm2.2.1-11amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye2.2.1-11amd64,arm64,armhf,i386
Debtags of package dialign:
biologyformat:aln, nuceleic-acids, peptidic
fieldbiology, biology:bioinformatics
interfacecommandline
roleprogram
scopeutility
useanalysing, comparing
works-with-formatplaintext
Popcon: 12 users (38 upd.)*
Versions and Archs
 License: DFSG free
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 :-(
Versions of package dialign-tx
ReleaseVersionArchitectures
bullseye1.0.2-13amd64,arm64,armhf,i386
trixie1.0.2-15amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky1.0.2-15amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm1.0.2-14amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid1.0.2-15amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
Debtags of package dialign-tx:
fieldbiology, biology:bioinformatics
roleprogram
scopeutility
usecomparing
works-with-formatplaintext
Popcon: 11 users (36 upd.)*
Versions and Archs
 License: DFSG free
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 
exonerate
??? missing short description for package exonerate :-(
Versions of package exonerate
ReleaseVersionArchitectures
forky2.4.0-5amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm2.4.0-5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie2.4.0-5amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid2.4.0-5amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye2.4.0-5amd64,arm64,armhf,i386
Debtags of package exonerate:
fieldbiology, biology:bioinformatics
interfacecommandline
roleprogram
scopeutility
usesearching
works-with-formatplaintext
Popcon: 134 users (23 upd.)*
Versions and Archs
 License: DFSG free
Git
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 
fastdnaml
??? missing short description for package fastdnaml :-(
Versions of package fastdnaml
ReleaseVersionArchitectures
bookworm1.2.2-15amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky1.2.2-18amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid1.2.2-18amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye1.2.2-15amd64,arm64,armhf,i386
trixie1.2.2-18amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
Debtags of package fastdnaml:
fieldbiology, biology:bioinformatics
interfacecommandline
roleprogram
scopeutility
useanalysing, comparing
works-with-formatplaintext
Popcon: 8 users (34 upd.)*
Versions and Archs
 License: DFSG free
Git
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)
fasttree
??? missing short description for package fasttree :-(
Versions of package fasttree
ReleaseVersionArchitectures
bullseye2.1.11-2amd64,arm64,armhf,i386
trixie2.1.11-2amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm2.1.11-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid2.1.11-2amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky2.1.11-2amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
Popcon: 8 users (33 upd.)*
Versions and Archs
 License: DFSG free
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 
figtree
??? missing short description for package figtree :-(
Versions of package figtree
ReleaseVersionArchitectures
forky1.4.4-7all
bookworm1.4.4-5all
bullseye1.4.4-5all
sid1.4.4-7all
trixie1.4.4-6all
Popcon: 9 users (42 upd.)*
Versions and Archs
 License: DFSG free
Git
Registry entries: Bio.tools  SciCrunch  Bioconda 
gmap
??? missing short description for package gmap :-(
Versions of package gmap
ReleaseVersionArchitectures
trixie2024-11-20+ds-2amd64,arm64,armel,armhf,i386,ppc64el,riscv64
bullseye2021-02-22+ds-1amd64,arm64,armhf,i386
sid2025-07-31+ds-1amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
forky2025-07-31+ds-1amd64,arm64,armhf,i386,loong64,ppc64el,riscv64
bookworm2021-12-17+ds-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el
upstream2025-07-31.v2
Debtags of package gmap:
fieldbiology, biology:bioinformatics, biology:structural
roleprogram
useanalysing
Popcon: 8 users (34 upd.)*
Newer upstream!
 License: DFSG free
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 
hmmer
??? missing short description for package hmmer :-(
Versions of package hmmer
ReleaseVersionArchitectures
trixie3.4+dfsg-2amd64,arm64,i386
sid3.4+dfsg-3amd64,arm64,i386
forky3.4+dfsg-3amd64,arm64,i386
bullseye3.3.2+dfsg-1amd64,i386
bookworm3.3.2+dfsg-1amd64,i386
Debtags of package hmmer:
biologyformat:aln, peptidic
fieldbiology, biology:bioinformatics
interfacecommandline
roleprogram
scopeutility
usesearching
works-withdb
works-with-formatplaintext
Popcon: 34 users (36 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: S. R. Eddy: Profile hidden Markov models. (PubMed,eprint) Bioinformatics 14(9):755-763 (1998)
Registry entries: Bio.tools  SciCrunch  Bioconda 
Screenshots of package hmmer
iqtree
??? missing short description for package iqtree :-(
Versions of package iqtree
ReleaseVersionArchitectures
bookworm2.0.7+dfsg-1amd64,i386
forky2.4.0+dfsg-1amd64
trixie2.0.7+dfsg-1amd64,i386
bullseye1.6.12+dfsg-1amd64,i386
sid2.4.0+dfsg-1amd64
Popcon: 7 users (36 upd.)*
Versions and Archs
 License: DFSG free
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 
jmodeltest
??? missing short description for package jmodeltest :-(
Versions of package jmodeltest
ReleaseVersionArchitectures
bullseye2.1.10+dfsg-10all
sid2.1.10+dfsg-13all
forky2.1.10+dfsg-13all
bookworm2.1.10+dfsg-12all
Popcon: 0 users (0 upd.)*
Versions and Archs
 License: DFSG free
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 
kalign
??? missing short description for package kalign :-(
Versions of package kalign
ReleaseVersionArchitectures
trixie3.4.0-1amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky3.5.1-1amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid3.5.1-1amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye3.3-1amd64,arm64,armhf,i386
bookworm3.3.5-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package kalign:
biologyformat:aln, nuceleic-acids, peptidic
fieldbiology, biology:bioinformatics
interfacecommandline
roleprogram
scopeutility
usecomparing
works-with-formatplaintext
Popcon: 17 users (50 upd.)*
Versions and Archs
 License: DFSG free
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 
mrbayes
??? missing short description for package mrbayes :-(
Versions of package mrbayes
ReleaseVersionArchitectures
bookworm3.2.7a-6amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye3.2.7a-4amd64,arm64,armhf,i386
sid3.2.7a-7amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie3.2.7a-7amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
Popcon: 9 users (33 upd.)*
Versions and Archs
 License: DFSG free
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 
Screenshots of package mrbayes
muscle
??? missing short description for package muscle :-(
Versions of package muscle
ReleaseVersionArchitectures
bullseye3.8.1551-2amd64,arm64,armhf,i386
sid5.1.0-1amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky5.1.0-1amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie5.1.0-1amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm5.1.0-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream5.3
Debtags of package muscle:
biologyformat:aln, nuceleic-acids, peptidic
fieldbiology, biology:bioinformatics
interfacecommandline
roleprogram
scopeutility
usecomparing
works-with-formatplaintext
Popcon: 19 users (41 upd.)*
Newer upstream!
 License: DFSG free
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
Screenshots of package muscle
muscle3
??? missing short description for package muscle3 :-(
Versions of package muscle3
ReleaseVersionArchitectures
bookworm3.8.1551-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie3.8.1551-3amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky3.8.1551-3amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid3.8.1551-3amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
Popcon: 0 users (0 upd.)*
Versions and Archs
 License: DFSG free
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 :-(
Versions of package mustang
ReleaseVersionArchitectures
trixie3.2.4-1amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye3.2.3-4amd64,arm64,armhf,i386
forky3.2.4-1amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid3.2.4-1amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm3.2.4-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package mustang:
biologypeptidic
fieldbiology, biology:bioinformatics
interfacecommandline
roleprogram
useanalysing, comparing
works-with-formatplaintext
Popcon: 14 users (36 upd.)*
Versions and Archs
 License: DFSG free
Git
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 
Screenshots of package mustang
njplot
??? missing short description for package njplot :-(
Versions of package njplot
ReleaseVersionArchitectures
bullseye2.4-9amd64,arm64,armhf,i386
sid2.4-9amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie2.4-9amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm2.4-9amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky2.4-9amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
Debtags of package njplot:
fieldbiology, biology:bioinformatics
interfacex11
roleprogram
scopeutility
uitoolkitmotif
useanalysing, editing, organizing, printing, viewing
works-withbiological-sequence
works-with-formatplaintext
x11application
Popcon: 9 users (34 upd.)*
Versions and Archs
 License: DFSG free
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 
Screenshots of package njplot
phylip
??? missing short description for package phylip :-(
Versions of package phylip
ReleaseVersionArchitectures
sid3.697+dfsg-4amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie3.697+dfsg-4amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky3.697+dfsg-4amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm3.697+dfsg-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye3.697+dfsg-2amd64,arm64,armhf,i386
upstream3.698
Debtags of package phylip:
fieldbiology, biology:bioinformatics
interfacecommandline
roleprogram
scopeutility
useanalysing, comparing
works-with-formatplaintext
Popcon: 15 users (37 upd.)*
Newer upstream!
 License: DFSG free
Git
Registry entries: Bio.tools  SciCrunch  Bioconda 
phyml
??? missing short description for package phyml :-(
Versions of package phyml
ReleaseVersionArchitectures
bookworm3.3.20220408-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky3.3.20250515-2amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
sid3.3.20250515-2amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye3.3.20200621-1amd64,arm64,armhf,i386
trixie3.3.20220408-4amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
Debtags of package phyml:
biologypeptidic
fieldbiology, biology:bioinformatics
interfacecommandline
roleprogram
useanalysing, comparing
works-withbiological-sequence
Popcon: 14 users (38 upd.)*
Versions and Archs
 License: DFSG free
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 
Screenshots of package phyml
poa
??? missing short description for package poa :-(
Versions of package poa
ReleaseVersionArchitectures
bullseye2.0+20060928-8amd64,arm64,armhf,i386
bookworm2.0+20060928-8amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie2.0+20060928-10amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky2.0+20060928-10amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid2.0+20060928-10amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
Debtags of package poa:
fieldbiology, biology:bioinformatics
interfacecommandline
roleprogram
scopeutility
works-with-formatplaintext
Popcon: 12 users (36 upd.)*
Versions and Archs
 License: DFSG free
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 
Screenshots of package poa
populations
??? missing short description for package populations :-(
Versions of package populations
ReleaseVersionArchitectures
sid1.2.33+svn0120106+dfsg-8amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye1.2.33+svn0120106+dfsg-6amd64,arm64,armhf,i386
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pplacer
??? missing short description for package pplacer :-(
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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)
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proalign
??? missing short description for package proalign :-(
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Please cite: Ari Löytynoja and Michel C Milinkovitch: A hidden Markov model for progressive multiple alignment. (PubMed,eprint) Bioinformatics 19(12):1505-13 (2003)
probalign
??? missing short description for package probalign :-(
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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)
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probcons
??? missing short description for package probcons :-(
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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)
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proda
??? missing short description for package proda :-(
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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)
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prottest
??? missing short description for package prottest :-(
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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)
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quicktree
??? missing short description for package quicktree :-(
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seaview
??? missing short description for package seaview :-(
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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)
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sigma-align
??? missing short description for package sigma-align :-(
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Please cite: Siddharthan, Rahul: Sigma: multiple alignment of weakly-conserved non-coding DNA sequence. (PubMed) BMC Bioinformatics 7(1):143 (2006)
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spread-phy
??? missing short description for package spread-phy :-(
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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)
t-coffee
??? missing short description for package t-coffee :-(
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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)
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tm-align
??? missing short description for package tm-align :-(
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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)
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tree-ppuzzle
??? missing short description for package tree-ppuzzle :-(
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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)
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tree-puzzle
??? missing short description for package tree-puzzle :-(
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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)
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treeview
??? missing short description for package treeview :-(
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Please cite: Alok J. Saldanha: Java Treeview -- extensible visualization of microarray data. (PubMed,eprint) Bioinformatics 20(17):3246-3248 (2004)
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treeviewx
??? missing short description for package treeviewx :-(
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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)
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veryfasttree
??? missing short description for package veryfasttree :-(
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Official Debian packages with lower relevance

python3-treetime
??? missing short description for package python3-treetime :-(
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Packaging has started and developers might try the packaging code in VCS

forester
Graphical vizualiation tool Archaeopteryx
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Version: 0.0+20180205-1

Archaeopteryx is a software tool for the visualization, analysis, and editing of potentially large and highly annotated phylogenetic trees. It can be used both as applet (ArchaeopteryxA and ArchaeopteryxE) and as a standalone application.
patristic
Calculate patristic distances and comparing the components of genetic change
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Version: 0.0.20100817-2

Patristic overcomes some logistic barriers to analysing signals in sequences. In additional to calculating patristic distances, it provides plots for any combination of matrices, calculates commonly used statistics, allows data such as isolation dates to be entered and reorders matrices with matching species or gene labels. It will be used to analyse rates of mutation and substitutional saturation and the evolution of viruses.
Please cite: Mathieu Fourment and Mark J Gibbs: PATRISTIC: a program for calculating patristic distances and graphically comparing the components of genetic change. (PubMed,eprint) BMC Evolutionary Biology 6:1 (2006)

No known packages available but some record of interest (WNPP bug)

phylowin - wnpp
Graphical interface for molecular phylogenetic inference
License: unknown
Debian package not available

Phylo_win is a graphical colour interface for molecular phylogenetic inference. It performs neighbor-joining, parsimony and maximum likelihood methods and bootstrap with any of them. Many distances can be used including Jukes & Cantor, Kimura, Tajima & Nei, HKY, Galtier & Gouy (1995), LogDet for nucleotidic sequences, Poisson correction for protein sequences, Ka and Ks for codon sequences. Species and sites to include in the analysis are selected by mouse. Reconstructed trees can be drawn, edited, printed, stored and evaluated according to numerous criteria.

This program uses sources files from the Phylip program, which forbids its use for profit. Therfore, Phylo_win will unfortunately have to be distributed in contrib or non-free.
Remark of Debian Med team: Issuer of previous ITP said:

Because I could never figure out the license of Phylo_win, and because the upstream authors released SeaView 4, which provides similar functionalities, I will not package Phylo_win.

Probably it makes sense to remove this project from the prospective packages list.

No known packages available

gbioseq
DNA sequence editor for Linux
License: GPL
Debian package not available

gBioSeq is in an early stage of development, but it is already running. The goal is to provide an easy to use software to edit DNA sequences under Linux, Windows, MacOsX, using GTK C# (Mono).
jstreeview
Editor for Phylogenetic Trees
License: MIT/X11
Debian package not available
Language: JavaScript

A concise viewer/editor for phylogenetic trees in the Newick format. The core functions are written in JavaScript, using the canvas tag proposed by HTML 5. No server side support is needed for rendering the picture and therefore you can grab this page together with knhx.js and canvastext.js to locally view your trees in a supported web browser.

The source can be downloaded at http://www.sanger.ac.uk/Users/lh3/download/jstreeview.zip
phpphylotree
draw phylogenetic trees
License: GPL
Debian package not available

PhpPhylotree is a web application that is able to draw phylogenetic trees. It produces an SVG (Scalable Vector Graphic) file from phylip/newick tree files.
treetime
Bayesian sampling of phylogenetic trees from molecular data
License: GPL
Debian package not available

TreeTime is controlled by input files in nexus format and does bayesian sampling of phylogenetic trees from these data.
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 284154