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 method 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
BEAST Bayesian Evolutionary Analysis Sampling Trees Bayesian inference, relaxed molecular clock, demographic history download A. J. Drummond, A. Rambaut
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 Neighbor-joining, UPGMA, MrBayes plugin, PHYML plugin download 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
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 non-phylogenetic multivariate analysis. Maximum parsimony, distance matrix, maximum likelihood Mesquite home page W. P. 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.
Nona Phylogenetic inference Maximum parsimony, implied weighting, ratchet download P. Goloboff
PAML Phylogenetic analysis by maximum likelihood Maximum likelihood download Z. Yang
PAUP Phylogenetic analysis using parsimony 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
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
TNT Phylogenetic inference Parsimony, weighting, ratchet, tree drift, tree fusing, sectorial searches download P. Goloboff 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
TREE-PUZZLE Maximum likelihood and statistical analysis Maximum likelihood download H.A. Schmidt, K. Strimmer, A. von Haeseler
T-REX Tree inferring and visualization, Gene transfer detection Distance, Parsimony and Maximum likelihood T-REX server V. Makarenkov, et al.
Winclada GUI and tree editor (requires Nona) Maximum parsimony, ratchet download K. Nixon

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