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 DescriptionMethodsAuthor
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 supportIdentification 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 topologyPatrick Kück, Sandra A Meid, Christian Groß, Bernhard Misof, Johann Wolfgang Wägele.
ape [3]R-Project package for analysis of phylogenetics and evolutionProvides a large variety of phylogenetics functionsMaintainer: Emmanuel Paradis
Armadillo Workflow Platform [4] Workflow platform dedicated to phylogenetic and general bioinformatic analysisInference 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 phylogenyBayesian inference, alignment as well as tree search.M.A. Suchard, B. D. Redelings
BATWING [6] Bayesian Analysis of Trees With Internal Node GenerationBayesian inference, demographic history, population splitsI. J. Wilson, Weale, D.Balding
BayesPhylogenies [7] Bayesian inference of trees using Markov chain Monte Carlo methodsBayesian 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 availableTrait analysisM. Pagel, A. Meade
BEAST [9] Bayesian Evolutionary Analysis Sampling TreesBayesian inference, relaxed molecular clock, demographic historyA. J. Drummond, A. Rambaut & M. A. Suchard
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 alignmentsDistance and maximum likelihood methods (through phyml, phylip & tree-puzzle)S. Ramirez, E. Rodriguez.
BUCKy Bayesian concordance of gene treesBayesian concordance using modified greedy consensus of unrooted quartetsC. 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 alignmentDistance matrix/nearest neighborThompson et al.
Dendroscope [11] Tool for visualizing rooted trees and calculating rooted networksRooted trees, tanglegrams, consensus networks, hybridization networksDaniel Huson et al.
EzEditor [12] 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 JoiningJeon, Y.S. et al.
fastDNAml Optimized maximum likelihood (nucleotides only)Maximum likelihoodG.J. Olsen
FastTree 2[13] Fast phylogenetic inference for alignments with up to hundreds of thousands of sequencesApproximate maximum likelihoodM.N. Price, P.S. Dehal, A.P. Arkin
fitmodel Fits branch-site codon models without the need of prior knowledge of clades undergoing positive selectionMaximum likelihoodS. Guindon
Geneious Geneious provides genome and proteome research toolsNeighbor-joining, UPGMA, MrBayes plugin, PHYML plugin, RAxML plugin, FastTree plugin, GARLi plugin, PAUP* PluginA. J. Drummond,M.Suchard,V.Lefort et al.
HyPhy Hypothesis testing using phylogeniesMaximum likelihood, neighbor-joining, clustering techniques, distance matricesS.L. Kosakovsky Pond, S.D.W. Frost, S.V. Muse
IQPNNI Iterative ML treesearch with stopping ruleMaximum likelihood, neighbor-joiningL.S. Vinh, A. von Haeseler, B.Q. Minh
IQ-TREE [14] 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,[15] branch tests, tree topology tests, likelihood mappingLam-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 substitutionMaximum likelihood, AIC, BIC, DT, hLTR, dLTRD. Darriba, GL. Taboada, R. Doallo, D. Posada
LisBeth Three-item analysis for phylogenetics and biogeographyThree-item analysisJ. Ducasse, N. Cao & R. Zaragüeta-Bagils
MEGA Molecular Evolutionary Genetics AnalysisDistance, Parsimony and Maximum Composite Likelihood MethodsTamura 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 likelihoodWayne 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 likelihoodThomas Keane
MOLPHY Molecular phylogenetics (protein or nucleotide)Maximum likelihoodJ. Adachi and M. Hasegawa
MrBayes Posterior probability estimationBayesian inferenceJ. Huelsenbeck, et al.
Network Free Phylogenetic Network SoftwareMedian Joining, Reduced Median, Steiner NetworkA. Roehl
Nona Phylogenetic inferenceMaximum parsimony, implied weighting, ratchetP. Goloboff
PAML Phylogenetic analysis by maximum likelihoodMaximum likelihood and Bayesian inferenceZ. Yang
ParaPhylo [16] Computation of gene and species trees based on event-relations (orthology, paralogy)Cograph-Editing and Triple-InferenceHellmuth
PartitionFinder Combined selection of models of molecular evolution and partitioning schemes for DNA and protein alignments.Maximum likelihood, AIC, AICc, BICR. Lanfear, B Calcott, SYW Ho, S Guindon
PAUP* Phylogenetic analysis using parsimony (*and other methods)Maximum parsimony, distance matrix, maximum likelihoodD. Swofford
phangorn [17] Phylogenetic analysis in RML, MP, distance matrix, bootstrap, phylogentic networks, bootstrap, model selection, SH-test, SOWH-testMaintainer: K. Schliep
Phybase [18] an R package for species tree analysisphylogenetics functions, STAR, NJst, STEAC, maxtree, etcL. Liu & L. Yu
phyclust Phylogenetic Clustering (Phyloclustering)Maximum likelihood of Finite Mixture ModesWei-Chen Chen
PHYLIP Phylogenetic inference packageMaximum parsimony, distance matrix, maximum likelihoodJ. Felsenstein
phyloT Generates phylogenetic trees in various formats, based on NCBI taxonomynoneI. Letunic
PhyloQuart Quartet implementation (uses sequences or distances)Quartet methodV. 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 likelihoodMaximum likelihoodS. Guindon & O. Gascuel
phyx [19] Unix/GNU/Linux command line phylogenetic toolsExplore, 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, AlignmentA. 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 sequencesMaximum likelihood, AIC, BIC, DTD. Darriba, GL. Taboada, R. Doallo, D. Posada
PyCogent Software library for genomic biologySimulating sequences, alignment, controlling third party applications, workflows, querying databases, generating graphics and phylogenetic treesKnight et al.
QuickTree Tree construction optimized for efficiencyNeighbor-joiningK. Howe, A. Bateman, R. Durbin
RAxML-HPC Randomized Axelerated Maximum Likelihood for High Performance Computing (nucleotides and aminoacids)Maximum likelihood, simple Maximum parsimonyA. Stamatakis
RAxML-NG [20] Randomized Axelerated Maximum Likelihood for High Performance Computing (nucleotides and aminoacids) Next GenerationMaximum likelihood, simple Maximum parsimonyA. 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 methodM. Ninio, E. Privman, T. Pupko, N. Friedman
sowhat [21]Hypothesis testingSOWH testChurch, Ryan, and Dunn
SplitsTree [22] Tree and network programComputation, visualization and exploration of phylogenetic trees and networksD.H. Huson and D. Bryant
TNT Phylogenetic inferenceParsimony, weighting, ratchet, tree drift, tree fusing, sectorial searchesP. Goloboff et al.
TOPALi Phylogenetic inferencePhylogenetic model selection, Bayesian analysis and Maximum Likelihood phylogenetic tree estimation, detection of sites under positive selection, and recombination breakpoint location analysisIain Milne, Dominik Lindner et al.
TreeGen Tree construction given precomputed distance dataDistance matrixETH Zurich
TreeAlign Efficient hybrid methodDistance matrix and approximate parsimonyJ. Hein
Treefinder [23] 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 languageMaximum likelihood, distances, and othersJobb G, von Haeseler A, Strimmer K
TREE-PUZZLE [24][25] Maximum likelihood and statistical analysisMaximum likelihoodMakarenkov
T-REX (Webserver) [26] Tree inference and visualization, Horizontal gene transfer detection, multiple sequence alignmentDistance (neighbor joining), Parsimony and Maximum likelihood (PhyML, RAxML) tree inference, MUSCLE, MAFFT and ClustalW sequence alignments and related applicationsBoc A, Diallo AB, Makarenkov V
UGENE Fast and free multiplatform tree editorbased Phylip 3.6 package algorithmsUnipro
Winclada GUI and tree editor (requires Nona)Maximum parsimony, ratchetK. Nixon
Xrate Phylo-grammar engineRate estimation, branch length estimation, alignment annotationI. 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. Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ (April 2014). "BEAST 2: a software platform for Bayesian evolutionary analysis". PLoS Computational Biology. 10 (4): e1003537. Bibcode:2014PLSCB..10E3537B. doi:10.1371/journal.pcbi.1003537. PMC 3985171. PMID 24722319.
  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. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. Schliep KP (February 2011). "phangorn: phylogenetic analysis in R". Bioinformatics. 27 (4): 592–3. doi:10.1093/bioinformatics/btq706. PMC 3035803. PMID 21169378.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
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