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, 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 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.[11]
Dendroscope [12] Tool for visualizing rooted trees and calculating rooted networksRooted trees, tanglegrams, consensus networks, hybridization networksDaniel 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 JoiningJeon, Y.S. et al.
fastDNAml Optimized maximum likelihood (nucleotides only)Maximum likelihoodG.J. Olsen
FastTree 2[14] 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 [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 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
MorphoBank Web application to organize trait data (morphological characters) for tree building for use with Maximum Parsimony (via the CIPRES portal), Maximum Likelihood, and Bayesian analysis) O'Leary, M. A., and S. Kaufman,[17] also K. Alphonse
MrBayes Posterior probability estimationBayesian inferenceJ. Huelsenbeck, et al.[18]
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 [19] 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
PASTIS R package for phylogenetic assembly R, two‐stage Bayesian inference using MrBayes 3.2 Thomas et al. 2013[20]
PAUP* Phylogenetic analysis using parsimony (*and other methods)Maximum parsimony, distance matrix, maximum likelihoodD. Swofford
phangorn [21] Phylogenetic analysis in RML, MP, distance matrix, bootstrap, phylogentic networks, bootstrap, model selection, SH-test, SOWH-testMaintainer: K. Schliep
Phybase [22] 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 [23] 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 [24] 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 [25]Hypothesis testingSOWH testChurch, Ryan, and Dunn
SplitsTree [26] 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 [27] 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 [28][29] Maximum likelihood and statistical analysisMaximum likelihoodMakarenkov
T-REX (Webserver) [30] 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

References
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