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

• List of phylogenetic tree visualization software

References

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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.
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7. Pagel M, Meade A (2007), BayesPhylogenies 1.0. Software distributed by the authors.
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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.
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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