phylogeny
| Software | OS | Webserver | Comments |
|---|---|---|---|
| PAUP* | all | No | All-time classic! GUI is available for OS9 and Windows. |
| MEGA | Windows | No | Distance and parsimony. Various statistical tests of selection. Great alignment editor with NCBI BLAST capacity. |
| GARLI | all | Yes | Genetic Algorithm for Rapid Likelihood Inference. Very fast! |
| RAxML | all | BlackBox & CIPRES | Randomized Axelerated Maximum Likelihood for High Performance Computing. For large matrices, etc. Outputs sitewise likelihoods in Tree-Puzzle format for use in CONSEL. Starts ML optimization from random or MP trees. Does ELW. Accepts multiple outgroups. Spectacular user support, awesome and very fast! |
| PHYML | all | Yes | Fast for large phylogenies. Has customized versions for download on its website. |
| Treefinder | all | No | Phylogenetic inference using ML. A variety of special analysis tools including a test for compositional equilibrium, plotting of rate profiles along sequence alignments, and NPRS tree calibration. It is programmable in the functional and system-independent programming language, TL. |
| Tree-Puzzle | all | No | ML phylogenetic inference using quartet puzzling tree search. Does nucleotide, protein, and binary data. |
| PHYLIP | all | Pasteur & EBC | All-time classic! Distance, parsimony, and likelihood. |
| PhyloCoco | OSX | No | ML (GTR) and ME with general additive distances, very large-scale neighborhood, iterated local search, and ant colony optimization. |
| MrBayes | all | Yes | Bayesian inference of phylogeny accomodating multiple partitions (DNA, protein, morphology/binary). If an outgroup is not defined a priori, it assumes the first taxon is the outgroup. |
| BAMBE | UNIX & Windows | Yes | Bayesian analysis of phylogenies. |
| BayesPhylogenies | All | No | Bayesian analysis of phylogenies. Allows for a mixture model without partitioning and for multiple outgroups. |
| PhyloBayes | *nix | No | Bayesian MCMC phylogenetic reconstruction for protein sequences using the CAT mixture model. |
| LVB | all | Yes | Phylogenetic reconstruction using parsimony with a simulated annealing heuristic search. For moderately large data matrices. |
| TNT | all | No | Phylogenetic reconstruction using parsimony. The fastest MP program so far! |
| POY | all | No | Phylogenetic reconstruction using parsimony and ML (POYML). It uses Direct Optimization. |
| PAUPRat | all | No | PAUP implementation of the parsimony ratchet. See also a program for likelihood ratchet. |
| HyPhy | all | Yes | Handy for ML and hypothesis testing. Also tests for selection. Customizable through its batch language. |
| PHASE | Linux & Windows | No | RNA-oriented phylogenetic methods. |
| PROCOV | *nix | No | ML phylogeny under protein covarion models. |
| NETWORK | Windows | No | For median-joining networks; estimates TMRCA. |
| SplitsTree | all | No | Estimates median networks, parsimony splits, spectral analysis, split decomposition, neighbor-net, recombination networks, hybridization networks, standard tree reconstruction methods and the (refined) Buneman tree. |
| TCS | Windows | No | Estimates phylogenetic networks from DNA sequences or nucleotide distances using the statistical parsimony algorithm. |
| CombineTrees | all | No | Combines MP trees into a single (possibly reticulated) graph. |
| PhyloNet | all | No | Reconstructs of reticulate relationships. Infers horizontal gene transfer from a pair of species/gene trees and detects interspecific recombination breakpoints. Reads/stores/compares networks. |
| BEAST | all | No | For Bayesian estimation of TMRCA (among other things) in a strict or relaxed clock framework and evolutionary rates. |
| r8s | *nix | No | Estimates absolute rates of molecular evolution and divergence times on a phylogenetic tree. |
| Multidivtime | *nix | No | Studies rates of molecular evolution and estimates divergence times. |
| PATHd8 | All | No | Phylogenetic dating of large trees without a molecular clock. |
| Punctuated Evolution | all | Yes | Detects significant punctuated molecular evolution from phylogenetic trees. Where the punctuational effect is present the program will report the proportion of evolution attributable to speciation events (nodes). It also reports the deviation from the molecular clock caused by punctuational effects. |
| APE | R | No | Reads/writes/plots/manipulates trees; comparative data analyses in a phylogenetic framework; diversification rates and macroevolution; distances from allelic and nucleotide data; Mantel's test; minimum spanning tree; population parameter theta; nucleotide diversity; generalized skyline plot; estimation of absolute evolutionary rates and clock-like trees using NPRS and PL; classifies genes in trees using the Klastorin-Misawa-Tajima approach. NJ/ML phylogenies. |
| SymmeTREE | all | No | Implements several tests of differential diversification rates that exploit information on the topological distribution of species diversity throughout entire trees. |
| LASER | R | No | Implements ML methods based on the birth-death process to test whether diversification rates have changed over time. |
| Brownie | all | No | Analyzes rates of continuous character evolution and looking for substantial rate differences in different parts of a tree using LRT/AIC. |
| AxParafit & AxPcoords | all | No | Highly optimized/parallel versions of ParaFit and DistPCoA | .
| CopyCat | all | No | Tests cophylogenetic associations, wrapper for ParaFit. |
| gtp | *nix | No | Gene/species tree reconciliation and gene tree parsimony. |
| Notung | all | No | Provides a unified framework for incorporating duplication/loss parsimony in phylogenetic tasks. Gene/species trees reconciliation; gene duplication times in terms of speciation events; rearrange regions of a gene tree with weak support in the data to obtain alternate hypotheses |
| ParaFit | Windows & OS9 | No | Tests cophylogenetic associations. |
| PrIMETV | Linux | Yes | Visualizes tree-within-tree phenomena such as gene/species tree reconciliations. |
| Softparsmap | all | No | Maps gene trees onto species trees based on the soft parsimony method. |
| TreeFitter | all | No | Fits genetrees into species trees as well as combines trees in coevolutionary and biogeographic studies within an event-based parsimony context. |
| TreeMap | all | No | Parsimony-based cophylogeny mapping of host and parasite trees. |
| Cartographer | all | No | Mesquite module to plot the geographic location of taxa onto a calibrated map. |
| GeoPhyloBuilder | all | No | ARCGIS extension for creating 'geophylogenies'. |
| Phylogeographer | all | No | Test phylogeographic hypotheses (maps & genetic distances). |
| CONSEL | all | No | Assesses the confidence of phylogenetic tree selection. Approximately Unbiased, SH, weighted SH, KH test and their CIs. |
| BayesTraits | all | No | For trait evolution among groups of species for which a phylogeny or sample of phylogenies is available. Discrete and continuous characters. |
| bms_runner | all | No | Uses BayesTraits to predict functional links among genes, on the basis of correlated gain and loss of genes from species' genomes. |
| SIMMAP | OSX | No | A post-tree analysis program for making inferences based on sampling character histories from the posterior distribution of character histories on a phylogeny(ies). |
| BaTS | all | No | Tests for significant phylogeny-trait correlations taking into account uncertainty arising from phylogenetic error by integrating over the credible set of topologies produced by a bayesian estimation method such as BEAST or MrBayes. |
| More comparative methods programs | all | Maybe | See Joe Felsenstein's website |
Email me if you think a program should be listed here.