List of phylogenetics software


This list of phylogenetics software is a compilation of computational phylogenetics software used to produce phylogenetic trees. Such tools are commonly used in comparative genomics, cladistics, and bioinformatics. Methods for estimating phylogenies include neighbor-joining, maximum parsimony (also simply referred to as parsimony), UPGMA, Bayesian phylogenetic inference, maximum likelihood and distance matrix methods.

Name Description Methods Author
AncesTree [1] An algorithm for clonal tree reconstruction from multi-sample cancer sequencing data. Maximum Likelihood, Integer Linear Programming (ILP) M. El-Kebir, L. Oesper, H. Acheson-Field, and B. J. Raphael
AliGROOVE [2] Visualisation of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support Identification of single taxa which show predominately randomized sequence similarity in comparison with other taxa in a multiple sequence alignment and evaluation of the reliability of node support in a given topology Patrick Kück, Sandra A Meid, Christian Groß, Bernhard Misof, Johann Wolfgang Wägele.
ape [3] R-Project package for analysis of phylogenetics and evolution Provides a large variety of phylogenetics functions Maintainer: Emmanuel Paradis
Armadillo Workflow Platform [4] Workflow platform dedicated to phylogenetic and general bioinformatic analysis Inference of phylogenetic trees using Distance, Maximum Likelihood, Maximum Parsimony, Bayesian methods and related workflows. E. Lord, M. Leclercq, A. Boc, A.B. Diallo and V. Makarenkov
BAli-Phy [5] Simultaneous Bayesian inference of alignment and phylogeny Bayesian inference, alignment as well as tree search. M.A. Suchard, B. D. Redelings
BATWING [6] Bayesian Analysis of Trees With Internal Node Generation Bayesian inference, demographic history, population splits I. J. Wilson, Weale, D.Balding
BayesPhylogenies [7] Bayesian inference of trees using Markov chain Monte Carlo methods Bayesian inference, multiple models, mixture model (auto-partitioning) M. Pagel, A. Meade
BayesTraits [8] Analyses trait evolution among groups of species for which a phylogeny or sample of phylogenies is available Trait analysis M. Pagel, A. Meade
BEAST [9] Bayesian Evolutionary Analysis Sampling Trees Bayesian inference, relaxed molecular clock, demographic history A. J. Drummond, M. A. Suchard, D Xie & A. Rambaut
BioNumerics Universal platform for the management, storage and analysis of all types of biological data, including tree and network inference of sequence data. Neighbor-joining, maximum parsimony, UPGMA, maximum likelihood, distance matrix methods,... Calculation of the reliability of trees/branches using bootstrapping, permutation resampling or error resampling. L. Vauterin & P. Vauterin.
Bosque Integrated graphical software to perform phylogenetic analyses, from the importing of sequences to the plotting and graphical edition of trees and alignments Distance and maximum likelihood methods (through phyml, phylip & tree-puzzle) S. Ramirez, E. Rodriguez.
BUCKy Bayesian concordance of gene trees Bayesian concordance using modified greedy consensus of unrooted quartets C. Ané, B. Larget, D.A. Baum, S.D. Smith, A. Rokas and B. Larget, S.K. Kotha, C.N. Dewey, C. Ané
Canopy [10] Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing Maximum Likelihood, Markov Chain Monte Carlo (MCMC) methods Y. Jiang, Y. Qiu, A. J. Minn, and N. R. Zhang
CITUP Clonality Inference in Tumors Using Phylogeny Exhaustive search, Quadratic Integer Programming (QIP) S. Malikic, A.W. McPherson, N. Donmez, C.S. Sahinalp
ClustalW Progressive multiple sequence alignment Distance matrix/nearest neighbor Thompson et al.[11]
Dendroscope [12] Tool for visualizing rooted trees and calculating rooted networks Rooted trees, tanglegrams, consensus networks, hybridization networks Daniel Huson et al.
EzEditor [13] EzEditor is a java-based sequence alignment editor for rRNA and protein coding genes. It allows manipulation of both DNA and protein sequence alignments for phylogenetic analysis. Neighbor Joining Jeon, Y.S. et al.
fastDNAml Optimized maximum likelihood (nucleotides only) Maximum likelihood G.J. Olsen
FastTree 2[14] Fast phylogenetic inference for alignments with up to hundreds of thousands of sequences Approximate maximum likelihood M.N. Price, P.S. Dehal, A.P. Arkin
fitmodel Fits branch-site codon models without the need of prior knowledge of clades undergoing positive selection Maximum likelihood S. Guindon
Geneious Geneious provides genome and proteome research tools Neighbor-joining, UPGMA, MrBayes plugin, PHYML plugin, RAxML plugin, FastTree plugin, GARLi plugin, PAUP* Plugin A. J. Drummond,M.Suchard,V.Lefort et al.
HyPhy Hypothesis testing using phylogenies Maximum likelihood, neighbor-joining, clustering techniques, distance matrices S.L. Kosakovsky Pond, S.D.W. Frost, S.V. Muse
IQPNNI Iterative ML treesearch with stopping rule Maximum likelihood, neighbor-joining L.S. Vinh, A. von Haeseler, B.Q. Minh
IQ-TREE [15] An efficient phylogenomic software by maximum likelihood, as successor of IQPNNI and TREE-PUZZLE. Maximum likelihood, model selection, partitioning scheme finding, AIC, AICc, BIC, ultrafast bootstrapping,[16] branch tests, tree topology tests, likelihood mapping Lam-Tung Nguyen, O. Chernomor, H.A. Schmidt, A. von Haeseler, B.Q. Minh
jModelTest 2 A high-performance computing program to carry out statistical selection of best-fit models of nucleotide substitution Maximum likelihood, AIC, BIC, DT, hLTR, dLTR D. Darriba, GL. Taboada, R. Doallo, D. Posada
LisBeth Three-item analysis for phylogenetics and biogeography Three-item analysis J. Ducasse, N. Cao & R. Zaragüeta-Bagils
MEGA Molecular Evolutionary Genetics Analysis Distance, Parsimony and Maximum Composite Likelihood Methods Tamura K, Dudley J, Nei M & Kumar S
Mesquite Mesquite is software for evolutionary biology, designed to help biologists analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern comparative analyses or population genetics, while others do non-phylogenetic multivariate analysis. It can also be used to build timetrees incorporating a geological timescale, with some optional modules. Maximum parsimony, distance matrix, maximum likelihood Wayne Maddison and D. R. Maddison
MetaPIGA2 Maximum likelihood phylogeny inference multi-core program for DNA and protein sequences, and morphological data. Analyses can be performed using an extensive and user-friendly graphical interface or by using batch files. It also implements tree visualization tools, ancestral sequences, and automated selection of best substitution model and parameters. Maximum likelihood, stochastic heuristics (genetic algorithm, metapopulation genetic algorithm, simulated annealing, etc.), discrete Gamma rate heterogeneity, ancestral state reconstruction, model testing. Michel C. Milinkovitch and Raphaël Helaers
Modelgenerator Model selection (protein or nucleotide) Maximum likelihood Thomas Keane
MOLPHY Molecular phylogenetics (protein or nucleotide) Maximum likelihood J. Adachi and M. Hasegawa
MrBayes Posterior probability estimation Bayesian inference J. Huelsenbeck, et al.[17]
Network Free Phylogenetic Network Software Median Joining, Reduced Median, Steiner Network A. Roehl
Nona Phylogenetic inference Maximum parsimony, implied weighting, ratchet P. Goloboff
PAML Phylogenetic analysis by maximum likelihood Maximum likelihood and Bayesian inference Z. Yang
ParaPhylo [18] Computation of gene and species trees based on event-relations (orthology, paralogy) Cograph-Editing and Triple-Inference Hellmuth
PartitionFinder Combined selection of models of molecular evolution and partitioning schemes for DNA and protein alignments. Maximum likelihood, AIC, AICc, BIC R. Lanfear, B Calcott, SYW Ho, S Guindon
PASTIS R package for phylogenetic assembly R, two‐stage Bayesian inference using MrBayes 3.2 Thomas et al. 2013[19]
PAUP* Phylogenetic analysis using parsimony (*and other methods) Maximum parsimony, distance matrix, maximum likelihood D. Swofford
phangorn [20] Phylogenetic analysis in R ML, MP, distance matrix, bootstrap, phylogentic networks, bootstrap, model selection, SH-test, SOWH-test Maintainer: K. Schliep
Phybase [21] an R package for species tree analysis phylogenetics functions, STAR, NJst, STEAC, maxtree, etc L. Liu & L. Yu
phyclust Phylogenetic Clustering (Phyloclustering) Maximum likelihood of Finite Mixture Modes Wei-Chen Chen
PHYLIP Phylogenetic inference package Maximum parsimony, distance matrix, maximum likelihood J. Felsenstein
phyloT Generates phylogenetic trees in various formats, based on NCBI taxonomy none I. Letunic
PhyloQuart Quartet implementation (uses sequences or distances) Quartet method V. Berry
PhyloWGS Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors MCMC A. G. Deshwar, S. Vembu, C. K. Yung, G. H. Jang, L. Stein, and Q. Morris
PhyML Fast and accurate estimation of phylogenies using maximum likelihood Maximum likelihood S. Guindon & O. Gascuel
phyx [22] Unix/GNU/Linux command line phylogenetic tools Explore, manipulate, analyze, and simulate phylogenetic objects (alignments, trees, and MCMC logs) J.W. Brown, J.F. Walker, and S.A. Smith
POY A phylogenetic analysis program that supports multiple kinds of data and can perform alignment and phylogeny inference. A variety of heuristic algorithms have been developed for this purpose. Maximum parsimony, Maximum likelihood, Chromosome rearrangement, discreet characters, continuous characters, Alignment A. Varon, N. Lucaroni, L. Hong, W. Wheeler
ProtTest 3 A high-performance computing program for selecting the model of protein evolution that best fits a given set of aligned sequences Maximum likelihood, AIC, BIC, DT D. Darriba, GL. Taboada, R. Doallo, D. Posada
PyCogent Software library for genomic biology Simulating sequences, alignment, controlling third party applications, workflows, querying databases, generating graphics and phylogenetic trees Knight et al.
QuickTree Tree construction optimized for efficiency Neighbor-joining K. Howe, A. Bateman, R. Durbin
RAxML-HPC Randomized Axelerated Maximum Likelihood for High Performance Computing (nucleotides and aminoacids) Maximum likelihood, simple Maximum parsimony A. Stamatakis
RAxML-NG [23] Randomized Axelerated Maximum Likelihood for High Performance Computing (nucleotides and aminoacids) Next Generation Maximum likelihood, simple Maximum parsimony A. Kozlov, D. Darriba, T. Flouri, B. Morel, A. Stamatakis
SEMPHY Tree reconstruction using the combined strengths of maximum-likelihood (accuracy) and neighbor-joining (speed). SEMPHY has become outdated. The authors now refer users to RAxML, which is superior in both accuracy and speed. A hybrid maximum-likelihood / neighbor-joining method M. Ninio, E. Privman, T. Pupko, N. Friedman
sowhat [24] Hypothesis testing SOWH test Church, Ryan, and Dunn
SplitsTree [25] Tree and network program Computation, visualization and exploration of phylogenetic trees and networks D.H. Huson and D. Bryant
TNT Phylogenetic inference Parsimony, weighting, ratchet, tree drift, tree fusing, sectorial searches P. Goloboff et al.
TOPALi Phylogenetic inference Phylogenetic model selection, Bayesian analysis and Maximum Likelihood phylogenetic tree estimation, detection of sites under positive selection, and recombination breakpoint location analysis Iain Milne, Dominik Lindner et al.
TreeGen Tree construction given precomputed distance data Distance matrix ETH Zurich
TreeAlign Efficient hybrid method Distance matrix and approximate parsimony J. Hein
Treefinder [26] Fast ML tree reconstruction, bootstrap analysis, model selection, hypothesis testing, tree calibration, tree manipulation and visualization, computation of sitewise rates, sequence simulation, many models of evolution (DNA, protein, rRNA, mixed protein, user-definable), GUI and scripting language Maximum likelihood, distances, and others Jobb G, von Haeseler A, Strimmer K
TREE-PUZZLE [27][28] Maximum likelihood and statistical analysis Maximum likelihood Makarenkov
T-REX (Webserver) [29] Tree inference and visualization, Horizontal gene transfer detection, multiple sequence alignment Distance (neighbor joining), Parsimony and Maximum likelihood (PhyML, RAxML) tree inference, MUSCLE, MAFFT and ClustalW sequence alignments and related applications Boc A, Diallo AB, Makarenkov V
UGENE Fast and free multiplatform tree editor based Phylip 3.6 package algorithms Unipro
Winclada GUI and tree editor (requires Nona) Maximum parsimony, ratchet K. Nixon
Xrate Phylo-grammar engine Rate estimation, branch length estimation, alignment annotation I. Holmes

See also


  1. ^ El-Kebir M, Oesper L, Acheson-Field H, Raphael BJ (June 2015). "Reconstruction of clonal trees and tumor composition from multi-sample sequencing data". Bioinformatics. 31 (12): i62-70. doi:10.1093/bioinformatics/btv261. PMC 4542783. PMID 26072510.
  2. ^ Kück P, Meid SA, Groß C, Wägele JW, Misof B (August 2014). "AliGROOVE--visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support". BMC Bioinformatics. 15: 294. doi:10.1186/1471-2105-15-294. PMC 4167143. PMID 25176556.
  3. ^ Paradis E, Claude J, Strimmer K (January 2004). "APE: Analyses of Phylogenetics and Evolution in R language". Bioinformatics. Oxford, England. 20 (2): 289–90. doi:10.1093/bioinformatics/btg412. PMID 14734327.
  4. ^ Lord E, Leclercq M, Boc A, Diallo AB, Makarenkov V (2012). "Armadillo 1.1: an original workflow platform for designing and conducting phylogenetic analysis and simulations". PLOS ONE. 7 (1): e29903. Bibcode:2012PLoSO...729903L. doi:10.1371/journal.pone.0029903. PMC 3256230. PMID 22253821.
  5. ^ Suchard MA, Redelings BD (August 2006). "BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny". Bioinformatics (Oxford, England). 22 (16): 2047–8. doi:10.1093/bioinformatics/btl175. PMID 16679334.
  6. ^ Wilson IJ, Weale ME, Balding DJ (June 2003). "Inferences from DNA data: population histories, evolutionary processes and forensic match probabilities". Journal of the Royal Statistical Society: Series A (Statistics in Society). 166 (2): 155–88. doi:10.1111/1467-985X.00264.
  7. ^ Pagel M, Meade A (2007), BayesPhylogenies 1.0. Software distributed by the authors.
  8. ^ Pagel M, Meade A (2007). "BayesTraits. Computer program and documentation". pp. 1216–23.
  9. ^ Drummond A, Suchard MA, Xie D, Rambaut A (2012). "Bayesian phylogenetics with BEAUti and the BEAST 1.7". Molecular Biology and Evolution. 29 (8): 1969–1973. doi:10.1093/molbev/mss075. PMC 3408070. PMID 22367748.
  10. ^ Jiang Y, Qiu Y, Minn AJ, Zhang NR (September 2016). "Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing". Proceedings of the National Academy of Sciences of the United States of America. 113 (37): E5528-37. doi:10.1073/pnas.1522203113. PMC 5027458. PMID 27573852.
  11. ^ Thompson, Julie D.; Gibson, Toby J.; Higgins, Des G. (August 2002). "Multiple sequence alignment using ClustalW and ClustalX". Current Protocols in Bioinformatics. Chapter 2: 2.3.1–2.3.22. doi:10.1002/0471250953.bi0203s00. ISSN 1934-340X. PMID 18792934.
  12. ^ Huson DH, Scornavacca C (December 2012). "Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks". Systematic Biology. 61 (6): 1061–7. doi:10.1093/sysbio/sys062. PMID 22780991.
  13. ^ Jeon YS, Lee K, Park SC, Kim BS, Cho YJ, Ha SM, Chun J (February 2014). "EzEditor: a versatile sequence alignment editor for both rRNA- and protein-coding genes". International Journal of Systematic and Evolutionary Microbiology. 64 (Pt 2): 689–91. doi:10.1099/ijs.0.059360-0. PMID 24425826.
  14. ^ Price MN, Dehal PS, Arkin AP (March 2010). "FastTree 2--approximately maximum-likelihood trees for large alignments". PLOS ONE. 5 (3): e9490. Bibcode:2010PLoSO...5.9490P. doi:10.1371/journal.pone.0009490. PMC 2835736. PMID 20224823.
  15. ^ Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ (January 2015). "IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies". Molecular Biology and Evolution. 32 (1): 268–74. doi:10.1093/molbev/msu300. PMC 4271533. PMID 25371430.
  16. ^ Minh BQ, Nguyen MA, von Haeseler A (May 2013). "Ultrafast approximation for phylogenetic bootstrap". Molecular Biology and Evolution. 30 (5): 1188–95. doi:10.1093/molbev/mst024. PMC 3670741. PMID 23418397.
  17. ^ Huelsenbeck, J. P.; Ronquist, F. (August 2001). "MRBAYES: Bayesian inference of phylogenetic trees". Bioinformatics (Oxford, England). 17 (8): 754–755. doi:10.1093/bioinformatics/17.8.754. ISSN 1367-4803. PMID 11524383.
  18. ^ Hellmuth M, Wieseke N, Lechner M, Lenhof HP, Middendorf M, Stadler PF (February 2015). "Phylogenomics with paralogs". Proceedings of the National Academy of Sciences of the United States of America. 112 (7): 2058–63. arXiv:1712.06442. Bibcode:2015PNAS..112.2058H. doi:10.1073/pnas.1412770112. PMC 4343152. PMID 25646426.
  19. ^ Thomas, Gavin H.; Hartmann, Klaas; Jetz, Walter; Joy, Jeffrey B.; Mimoto, Aki; Mooers, Arne O. (2013). "PASTIS: an R package to facilitate phylogenetic assembly with soft taxonomic inferences". Methods in Ecology and Evolution. 4 (11): 1011–1017. doi:10.1111/2041-210X.12117. ISSN 2041-210X.
  20. ^ Schliep KP (February 2011). "phangorn: phylogenetic analysis in R". Bioinformatics. 27 (4): 592–3. doi:10.1093/bioinformatics/btq706. PMC 3035803. PMID 21169378.
  21. ^ Liu L, Yu L (April 2010). "Phybase: an R package for species tree analysis". Bioinformatics. 26 (7): 962–3. doi:10.1093/bioinformatics/btq062. PMID 20156990.
  22. ^ Brown JW, Walker JF, Smith SA (June 2017). "Phyx: phylogenetic tools for unix". Bioinformatics. 33 (12): 1886–1888. doi:10.1093/bioinformatics/btx063. PMC 5870855. PMID 28174903.
  23. ^ Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A (May 2019). "RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference". Bioinformatics. 35 (21): 4453–4455. doi:10.1093/bioinformatics/btz305. PMC 6821337. PMID 31070718.
  24. ^ Church SH, Ryan JF, Dunn CW (November 2015). "Automation and Evaluation of the SOWH Test with SOWHAT". Systematic Biology. 64 (6): 1048–58. doi:10.1093/sysbio/syv055. PMC 4604836. PMID 26231182.
  25. ^ Huson DH, Bryant D (February 2006). "Application of phylogenetic networks in evolutionary studies". Molecular Biology and Evolution. 23 (2): 254–67. doi:10.1093/molbev/msj030. PMID 16221896.
  26. ^ Jobb G, von Haeseler A, Strimmer K (June 2004). "TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics". BMC Evolutionary Biology. 4: 18. doi:10.1186/1471-2148-4-18. PMC 459214. PMID 15222900.
  27. ^ Makarenkov V (July 2001). "T-REX: reconstructing and visualizing phylogenetic trees and reticulation networks". Bioinformatics (Oxford, England). 17 (7): 664–8. doi:10.1093/bioinformatics/17.7.664. PMID 11448889.
  28. ^ Schmidt HA, Strimmer K, Vingron M, von Haeseler A (March 2002). "TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing". Bioinformatics (Oxford, England). 18 (3): 502–4. doi:10.1093/bioinformatics/18.3.502. PMID 11934758.
  29. ^ Boc A, Diallo AB, Makarenkov V (July 2012). "T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks". Nucleic Acids Research. 40 (Web Server issue): W573–9. doi:10.1093/nar/gks485. PMC 3394261. PMID 22675075.

External links

  • Complete list of Institut Pasteur phylogeny webservers
  • ExPASy List of phylogenetics programs
  • A very comprehensive list of phylogenetic tools (reconstruction, visualization, etc.)
  • Another list of evolutionary genetics software
  • A list of phylogenetic software provided by the Zoological Research Museum A. Koenig