| Name | Description | Methods | Link | Author |
|---|
| Armadillo Workflow Platform | Workflow platform dedicated to phylogenetic and general bioinformatic analysis | Inference of phylogenetic trees using Distance, Maximum Likelihood, Maximum Parsimony, Bayesian methods and related workflows. | homepage | E. Lord, M. Leclercq, A. Boc, A.B. Diallo and V. Makarenkov |
| BAli-Phy | Simultaneous Bayesian inference of alignment and phylogeny | Bayesian inference, alignment as well as tree search. | homepage | M.A. Suchard, B. D. Redelings |
| BATWING | Bayesian Analysis of Trees With Internal Node Generation | Bayesian inference, demographic history, population splits | download | I. J. Wilson, Weale, D.Balding |
| BayesPhylogenies | Bayesian inference of trees using Markov Chain Monte Carlo methods | Bayesian inference, multiple models, mixture model (auto-partitioning) | download | M. Pagel, A. Meade |
| BayesTraits | Analyses trait evolution among groups of species for which a phylogeny or sample of phylogenies is available | Trait analysis | download | M. Pagel, A. Meade |
| BEAST | Bayesian Evolutionary Analysis Sampling Trees | Bayesian inference, relaxed molecular clock, demographic history | download or development & download | A. J. Drummond, A. Rambaut & M. A. Suchard |
| 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. |
| BUCKy | Bayesian concordance of gene trees | Bayesian concordance using modified greedy consensus of unrooted quartets | stat.wisc.edu | C. Ané, B. Larget, D.A. Baum, S.D. Smith, A. Rokas and B. Larget, S.K. Kotha, C.N. Dewey, C. Ané |
| 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 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 |
| jModelTest 2 | A high-performance computing program to carry out statistical selection of best-fit models of nucleotide substitution | Maximum likelihood, AIC, BIC, DT, hLTR, dLTR | Repository | D. Darriba, GL. Taboada, R. Doallo, D. Posada |
| LisBeth | Three-item analysis for phylogenetics and biogeography | Three-item analysis | download | J. Ducasse, N. Cao & R. Zaragüeta-Bagils |
| 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 | Wayne Maddison and D. R. Maddison |
| MetaPIGA2 | Maximum likelihood phylogeny inference multi-core program for DNA and protein sequences, and morphological data. Analyses can be performed using an extensive and user-friendly graphical interface or by using batch files. It also implements tree visualization tools, ancestral sequences, and automated selection of best substitution model and parameters. | Maximum likelihood, stochastic heuristics (genetic algorithm, metapopulation genetic algorithm, simulated annealing, etc.), discrete Gamma rate heterogeneity, ancestral state reconstruction, model testing. | homepage | Michel C. Milinkovitch and Raphaël Helaers |
| Modelgenerator | Model selection (protein or nucleotide) | Maximum likelihood | download | Thomas Keane |
| 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 and Bayesian inference | download | Z. Yang |
| PartitionFinder | Combined selection of models of molecular evolution and partitioning schemes for DNA and protein alignments. | Maximum likelihood, AIC, AICc, BIC | download | R. Lanfear, B Calcott, SYW Ho, S Guindon |
| PAUP* | Phylogenetic analysis using parsimony (*and other methods) | Maximum parsimony, distance matrix, maximum likelihood | purchase | D. Swofford |
| phyclust | Phylogenetic Clustering (Phyloclustering) | Maximum likelihood of Finite Mixture Modes | download or homepage | Wei-Chen Chen |
| 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 |
| POY | A phylogenetic analysis program that supports multiple kinds of data and can perform alignment and phylogeny inference. A variety of heuristic algorithms have been developed for this purpose. | Maximum parsimony, Maximum likelihood, Chromosome rearrangement, discreet characters, continuous characters, Alignment | download | A. Varon, N. Lucaroni, L. Hong, W. Wheeler |
| ProtTest 3 | A high-performance computing program for selecting the model of protein evolution that best fits a given set of aligned sequences | Maximum likelihood, AIC, BIC, DT | Main page Repository | D. Darriba, GL. Taboada, R. Doallo, D. Posada |
| PyCogent | Software library for genomic biology | Simulating sequences, alignment, controlling third party applications, workflows, querying databases, generating graphics and phylogenetic trees | documentation/download | Knight et al. |
| 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 has become outdated. The authors now refer users to RAxML, which is superior in both accuracy and speed. | 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. |
| TOPALi | Phylogenetic inference | Phylogenetic model selection, Bayesian analysis and Maximum Likelihood phylogenetic tree estimation, detection of sites under positive selection, and recombination breakpoint location analysis | Main page download | Iain Milne, Dominik Lindner 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 (Webserver) | Tree inference and visualization, Horizontal gene transfer detection, multiple sequence alignment | Distance (neighbor joining), Parsimony and Maximum likelihood (PhyML, RAxML) tree inference, MUSCLE, MAFFT and ClustalW sequence alignments and related applications | T-REX server | V. Makarenkov, et al. |
| UGENE | Fast and free multiplatform tree editor | based Phylip 3.6 package algorithms | download | Unipro |
| 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 |
