List of Phylogenetic Softwares
From DrugPedia: A Wikipedia for Drug discovery
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 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 | |
| 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 & tree-puzzle) | download | S. Ramirez, E. Rodriguez. | |
| ClustalW | Progressive multiple sequence alignment | Distance matrix/nearest neighbor | EBI PBIL EMBNet GenomeNet | Thompson et al. | |
| Dendroscope | Tree drawing program | Visualization of large trees, consensus trees and networks | Dendroscope | D.H. Huson 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 | |
| Handel | Multiple sequence alignment using explicit indel and substitution models | Ancestral reconstruction, multiple sequence alignment, statistical alignment | homepage | I. Holmes | |
| 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. | |
| 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 | download | Z. Yang | |
| PAUP* (pronounced "pop star") | 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 | |
| SEMPHY | Tree reconstruction using the combined strengths of maximum-likelihood (accuracy) and neighbor-joining (speed). SEMPHY is especially advantageous for large datasets of hundreds and thousands of sequences, where a classical full maximum-likelihood analysis is too time-consuming. | A hybrid maximum-likelihood / neighbor-joining 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 | |
| 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, user-definable), GUI and scripting language | Maximum likelihood, distances, and others | download | G. Jobb | |
| 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 | |
| Xrate | Phylo-grammar engine | Rate estimation, branch length estimation, alignment annotation | homepage | I. Holmes |
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
Original source
This article is originally posted in Wikipedia.
