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
|