Surface of Mars from www.nasa.gov

phylogeny

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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.
Phycas all No Bayesian MCMC phylogenetic reconstruction for DNA sequences written in Python.
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.
Phangorn all No Phylogenetic analysis in R. Trees and networks, distance, Hadamard conjugation, ML, MP.
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.

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