List of phylogenetics software

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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 Link Author
ape R-Project package for analysis of phylogenetics and evolution Provides a large variety of phylogenetics functions homepage Maintainer: Emmanuel Paradis
Armadillo Workflow Platform Workflow platform dedicated to phylogenetic and general bioinformatic analysis Inference of phylogenetic trees using Distance, Maximum Likelihood, Maximum Parsimony, Bayesian methods and related workflows. homepage E. Lord, M. Leclercq, A. Boc, A.B. Diallo and V. Makarenkov
BAli-Phy Simultaneous Bayesian inference of alignment and phylogeny Bayesian inference, alignment as well as tree search. homepage M.A. Suchard, B. D. Redelings
BATWING Bayesian Analysis of Trees With Internal Node Generation Bayesian inference, demographic history, population splits download I. J. Wilson, Weale, D.Balding
BayesPhylogenies Bayesian inference of trees using Markov Chain Monte Carlo methods Bayesian inference, multiple models, mixture model (auto-partitioning) download M. Pagel, A. Meade
BayesTraits Analyses trait evolution among groups of species for which a phylogeny or sample of phylogenies is available Trait analysis download M. Pagel, A. Meade
BEAST Bayesian Evolutionary Analysis Sampling Trees Bayesian inference, relaxed molecular clock, demographic history download or development & download A. 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. Application page 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) download S. Ramirez, E. Rodriguez.
BUCKy Bayesian concordance of gene trees Bayesian concordance using modified greedy consensus of unrooted quartets stat.wisc.edu C. Ané, B. Larget, D.A. Baum, S.D. Smith, A. Rokas and B. Larget, S.K. Kotha, C.N. Dewey, C. Ané
ClustalW Progressive multiple sequence alignment Distance matrix/nearest neighbor EBI PBIL EMBNet GenomeNet Thompson et al.
EzEditor [1] 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 [1] Jeon, Y.S. et al.
fastDNAml Optimized maximum likelihood (nucleotides only) Maximum likelihood download G.J. Olsen
fitmodel Fits branch-site codon models without the need of prior knowledge of clades undergoing positive selection Maximum likelihood home page 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 [2] A. J. Drummond,M.Suchard,V.Lefort et al.
HyPhy Hypothesis testing using phylogenies Maximum likelihood, neighbor-joining, clustering techniques, distance matrices download S.L. Kosakovsky Pond, S.D.W. Frost, S.V. Muse
IQPNNI Iterative ML treesearch with stopping rule Maximum likelihood, neighbor-joining download L.S. Vinh, A. von Haeseler
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 Repository D. Darriba, GL. Taboada, R. Doallo, D. Posada
LisBeth Three-item analysis for phylogenetics and biogeography Three-item analysis download J. Ducasse, N. Cao & R. Zaragüeta-Bagils
MEGA Molecular Evolutionary Genetics Analysis Distance, Parsimony and Maximum Composite Likelihood Methods download 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 Mesquite home page 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. homepage Michel C. Milinkovitch and Raphaël Helaers
Modelgenerator Model selection (protein or nucleotide) Maximum likelihood download Thomas Keane
MOLPHY Molecular phylogenetics (protein or nucleotide) Maximum likelihood server J. Adachi and M. Hasegawa
MrBayes Posterior probability estimation Bayesian inference download J. Huelsenbeck, et al.
Network Free Phylogenetic Network Software Median Joining, Reduced Median, Steiner Network download A. Roehl
Nona Phylogenetic inference Maximum parsimony, implied weighting, ratchet download P. Goloboff
PAML Phylogenetic analysis by maximum likelihood Maximum likelihood and Bayesian inference download Z. Yang
PartitionFinder Combined selection of models of molecular evolution and partitioning schemes for DNA and protein alignments. Maximum likelihood, AIC, AICc, BIC download R. Lanfear, B Calcott, SYW Ho, S Guindon
PAUP* Phylogenetic analysis using parsimony (*and other methods) Maximum parsimony, distance matrix, maximum likelihood purchase D. Swofford
phyclust Phylogenetic Clustering (Phyloclustering) Maximum likelihood of Finite Mixture Modes download Wei-Chen Chen
PHYLIP Phylogenetic inference package Maximum parsimony, distance matrix, maximum likelihood download J. Felsenstein
PhyloQuart Quartet implementation (uses sequences or distances) Quartet method download V. Berry
PhyML Fast and accurate estimation of phylogenies using maximum likelihood Maximum likelihood home page S. Guindon & O. Gascuel
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 download 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 Main page Repository 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 documentation/download Knight et al.
QuickTree Tree construction optimized for efficiency Neighbor-joining server K. Howe, A. Bateman, R. Durbin
RAxML-HPC Randomized Axelerated Maximum Likelihood for High Performance Computing (nucleotides and aminoacids) Maximum likelihood, simple Maximum parsimony download 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 SEMPHY M. Ninio, E. Privman, T. Pupko, N. Friedman
SplitsTree Tree and network program Computation, visualization and exploration of phylogenetic trees and networks SplitsTree D.H. Huson and D. Bryant
TNT Phylogenetic inference Parsimony, weighting, ratchet, tree drift, tree fusing, sectorial searches download 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 Main page download Iain Milne, Dominik Lindner et al.
TreeGen Tree construction given precomputed distance data Distance matrix server ETH Zurich
TreeAlign Efficient hybrid method Distance matrix and approximate parsimony server J. Hein
Treefinder 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 download G. Jobb
TREE-PUZZLE Maximum likelihood and statistical analysis Maximum likelihood download H.A. Schmidt, K. Strimmer, A. von Haeseler
T-REX (Webserver) 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 T-REX server V. Makarenkov, et al.
UGENE Fast and free multiplatform tree editor based Phylip 3.6 package algorithms download Unipro
Winclada GUI and tree editor (requires Nona) Maximum parsimony, ratchet download K. Nixon
Xrate Phylo-grammar engine Rate estimation, branch length estimation, alignment annotation homepage I. Holmes

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References[edit]

  1. ^ Yoon-Seong Jeon, Kihyun Lee, Sang-Cheol Park, Bong-Soo Kim, Yong-Joon Cho, Sung-Min Ha and Jongsik Chun, 10.1099/ijs.0.059360-0 IJSEM December 2013 Int J Syst Evol Microbiol 64, 689-691

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