 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 neighborjoining, maximum parsimony (also simply referred to as parsimony), UPGMA, Bayesian phylogenetic inference, maximum likelihood and distance matrix methods.
Name Description Methods Link Author BAliPhy 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 (autopartitioning) 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 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 & treepuzzle) 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. fastDNAml Optimized maximum likelihood (nucleotides only) Maximum likelihood download G.J. Olsen Geneious Geneious provides sophisticated genome and proteome research tools Neighborjoining, UPGMA, MrBayes plugin, PHYML plugin download A. J. Drummond,M.Suchard,V.Lefort et al. HyPhy Hypothesis testing using phylogenies Maximum likelihood, neighborjoining, 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, neighborjoining download L.S. Vinh, A. von Haeseler LisBeth Threeitem analysis for phylogenetics and biogeography Threeitem analysis download J. Ducasse, N. Cao & R. ZaragüetaBagils 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 population genetics, while others do nonphylogenetic multivariate analysis. Maximum parsimony, distance matrix, maximum likelihood Mesquite home page Wayne Maddison and D. R. Maddison 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 PAUP* Phylogenetic analysis using parsimony (*and other methods) Maximum parsimony, distance matrix, maximum likelihood purchase D. Swofford 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 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 Neighborjoining server K. Howe, A. Bateman, R. Durbin RAxMLHPC 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 maximumlikelihood (accuracy) and neighborjoining (speed). SEMPHY has become outdated. The authors now refer users to RAxML, which is superior in both accuracy and speed. A hybrid maximumlikelihood / neighborjoining 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, userdefinable), GUI and scripting language Maximum likelihood, distances, and others download G. Jobb TREEPUZZLE Maximum likelihood and statistical analysis Maximum likelihood download H.A. Schmidt, K. Strimmer, A. von Haeseler TREX Tree inferring and visualization, Gene transfer detection Distance, Parsimony and Maximum likelihood TREX 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 Phylogrammar engine Rate estimation, branch length estimation, alignment annotation homepage I. Holmes See also
 List of phylogenetic tree visualization software
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
Categories: Bioinformatics
 Computational phylogenetics
 Lists of software
 Bioinformatics software
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Computational phylogenetics — is the application of computational algorithms, methods and programs to phylogenetic analyses. The goal is to assemble a phylogenetic tree representing a hypothesis about the evolutionary ancestry of a set of genes, species, or other taxa. For… … Wikipedia
Phylogenetic comparative methods — When applied to comparative data, conventional statistical methods assume, in effect, that all species are completely unrelated. As if they descended from a big bang of special creation. Such a scenario can be depicted as a star phylogeny (left) … Wikipedia
Quantitative comparative linguistics — is a branch of comparative linguistics that applies mathematical models to the problem of classifying language relatedness. This includes the use of computational phylogenetics and cladistics to define an optimal tree (or network) to represent a… … Wikipedia
Distance matrices in phylogeny — Distance matrices are used in phylogeny as non parametric distance methods were originally applied to phenetic data using a matrix of pairwise distances. These distances are then reconciled to produce a tree (a phylogram, with informative branch… … Wikipedia
Sequence alignment — In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences.[1]… … Wikipedia
Cladistics — For the scientific journal, see Cladistics (journal). Part of a series on Evolutionary Biology … Wikipedia
Cladogram — For help on how to use cladograms in Wikipedia, see Help:Cladograms A horizontal cladogram, with the ancestor (not named) to the left … Wikipedia
Computational — may refer to: Computer Computational algebra Computational Aeroacoustics Computational and Information Systems Laboratory Computational and Systems Neuroscience Computational archaeology Computational auditory scene analysis Computational biology … Wikipedia
Dendroscope — Dendroscope: (a) circular cladogram, (b) radial phylogram, (c) rectangular phylogram, and (d) slanted cladogram. Image by Huson et al. Developer(s) Daniel Huson et al. Stable release … Wikipedia
Mathematical and theoretical biology — is an interdisciplinary scientific research field with a range of applications in biology, medicine and biotechnology.[1] The field may be referred to as mathematical biology or biomathematics to stress the mathematical side, or as theoretical… … Wikipedia