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

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