List of phylogenetics software
From Wikipedia, the free encyclopedia
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.
| NAME | Description | Methods | Link | Author |
|---|---|---|---|---|
| PHYLIP | Phylogenetic inference package | Maximum parsimony, distance matrix, maximum likelihood | download | J. Felsenstein |
| Nona | Phylogenetic inference | Maximum parsimony, implied weighting, ratchet | download | P. Goloboff |
| Winclada | GUI and tree editor (requires Nona) | Maximum parsimony, ratchet | download | K. Nixon |
| TNT | Phylogenetic inference | Parsimony, weighting, ratchet, tree drift, tree fusing, sectorial searches | download | P. Goloboff et al |
| PAUP | Phylogenetic analysis using parsimony | Maximum parsimony, distance matrix, maximum likelihood | purchase | D. Swofford |
| PAML | Phylogenetic analysis by maximum likelihood | Maximum likelihood | download | Z. Yang |
| ClustalW | Progressive multiple sequence alignment | Distance matrix/nearest neighbor | EBI PBIL EMBNet GenomeNet | Thompson et al. |
| QuickTree | Tree construction optimized for efficiency | Neighbor-joining | server | K. Howe, A. Bateman, R. Durbin |
| MOLPHY | Molecular phylogenetics (protein or nucleotide) | Maximum likelihood | server | J. Adachi and M. Hasegawa |
| TreeGen | Tree construction given precomputed distance data | Distance matrix | server | ETH Zurich |
| fastDNAml | Optimized maximum likelihood (nucleotides only) | Maximum likelihood | download | G.J. Olsen |
| TREE-PUZZLE | Maximum likelihood and statistical analysis | Maximum likelihood | download | H.A. Schmidt, K. Strimmer, A. von Haeseler |
| TreeAlign | Efficient hybrid method | Distance matrix and approximate parsimony | server | J. Hein |
| PhyloQuart | Quartet implementation (uses sequences or distances) | Quartet method | download | V. Berry |
| MrBayes | Posterior probability estimation | Bayesian inference | download | J. Huelsenbeck, et al. |
| T-REX | Tree inferring and visualization, Gene transfer detection | Distance, Parsimony and Maximum likelihood | T-REX server | V. Makarenkov, 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 |
[edit] External links
- Complete list of Institut Pasteur phylogeny webservers
- ExPASy list of phylogenetics programs
