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molecular evolution

Software OS Webserver Comments
DnaSP Windows No All-time classic! Performs a multitude of tests and analyses, including coalescent simulations. Populations can be mouse-defined.
PAML all No A program package implementing a variety of sophisticated models of nucleotide and protein sequence evolution via ML. Allows to test alternative hypotheses using likelihood ratio tests. Not recommended for tree-building.
BEAST all No A program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards molecular clock analyses. It is not intended as a method of constructing phylogenies but rather testing evolutionary hypotheses without conditioning on a single tree topology. It uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability.
HyPhy all Yes Handy for ML and hypothesis testing. Also tests for selection. Customizable through its batch language.
FitModel all No Provides ML estimates of substitution model parameters of a phylogenetic tree and an alignment of homologous sequences. A broad range of Markov models of nucleotide and aminoacid substitutions are implemented. Coding sequences can also be analyzed under various codon-based substitution models. These models are especially useful as they accommodate site-specific switches between selection regimes.
SELECTON all Yes Server for the identification of site-specific positive selection & purifying selection.
Seq-Gen *nix No Simulates the evolution of nucleotide and aminoacid sequences along a phylogeny using a range of substitution models.
ModelTest all Yes Estimates the best-fitting model of DNA substitution among 56 models in conjunction with PAUP*. Uses AIC and also calculates model-averaged estimates and parameter importance. The FindModel webserver uses Weighbor, NJ, or MrBayes to generate the JC69 tree (does not allow for invariant sites). Also implemented in HyPhy.
jModelTest all No Carries out statistical selection of best-fit models of nucleotide substitution. It implements five different model selection strategies: hierarchical and dynamical likelihood ratio tests (hLRT and dLRT), Akaike and Bayesian information criteria (AIC and BIC), and a decision theory method (DT). It also provides estimates of model selection uncertainty, parameter importances and model-averaged parameter estimates, including model-averaged phylogenies.
MrAIC all No Estimates the best-fitting model of DNA substitution among 56/24 models in conjunction with PHYML. It differs with Modeltest in that it does not evaluate all models on the same topology, but rather uses PHYML to maximize the likelihood function for each model, which is needed for calculating AIC/AICc/AICw/BIC.
MrModelTest all No Estimates the best-fitting model of DNA substitution among 24 models that can be implemented in MrBayes in conjunction with PAUP*.
ProtTest all Yes Estimates the empirical model of aminoacid substitution fitting the data best among 64 models. Uses a BioNJ or user-defined starting tree. Can optimize parameters and the topology. Interacts with PHYML.
PartitionFinder all Yes Selects the best-fit partitioning schemes and models of molecular evolution for nucleotide and amino acid alignments. Interacts with PHYML.
TipDate *nix Yes ML estimation of evolutionary rates using heterochronous dated sequences. Also implemented in HyPhy by allowing for clock relaxation.
MAPPS OSX No Evaluates the fit of a group of phylogenetic models to DNA sequence data. The model's predictive ability is evaluated through simulation under the model. Comparison of simulated (or predictive data sets) is evaluated using the multinomial test statistic.
AWTY all Yes Evaluates the fit of a group of phylogenetic models to DNA sequence data. The model's predictive ability is evaluated through simulation under the model. Comparison of simulated (or predictive datasets) is evaluated using the multinomial test statistic.
K_Estimator Windows No Estimates the number of synonymous and nonsynonymous substitutions per site and their confidence intervals by Monte Carlo simulations.
HKA Windows & source No Carries out the HKA statistical test for natural selection and can handle very large numbers of loci and sample sizes, and conducts tests via coalescent simulations, as well as by the conventional chi-square approximation. The simulations can also be used to conduct other tests of natural selection, including Tajima's D (1989) and Fu & Li's D (1993).
NeutralityTest all Yes Performs various tests of neutrality.
PHASE Linux & Windows No RNA-based phylogenetic methods.
EvolveAGene all No Simulates coding DNA sequence evolution. Accounts for selective pressure and indels.
ReEVOLVER all No A tool to detect functional lineage-specific genes by evolutionary simulations.
FingerPrint all Yes Extracts and plots information (diversity, dn/ds, hydrophobicity, etc) from an alignment (nuc/aa).
t2prhd all Yes Generates simple diagrams that highlight relationships of sequence repeats detected by using a profile HMM in two sequences. Homology relations are identified on the basis of the phylogeny of repeats.

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