Bayesian Evolutionary Analysis Sampling Trees (BEAST) is a program for Bayesian Markov Chain Monte Carlo (MCMC) analysis of molecular sequences. It is oriented towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology.
Mesquite is a modular software system for evolutionary analysis, designed to help biologists analyze comparative data about organisms. Although its emphasis is on phylogenetic analysis, some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. The analyses include:
MrBayes is a program for doing Bayesian phylogenetic analysis including phylogenetic reconstruction. Bayesian inference of phylogeny is based on the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem.
PAUP* (Phylogenetic Analysis Using Parsimony *and other methods) is a program for phylogenetic analysis using parsimony, maximum likelihood, and distance methods. The program has a selection of analysis options and model choices, and accommodates DNA, RNA, protein and general data types. It has options for dealing with phylogenetic trees including importing, combining, comparing, constraining, rooting and testing hypotheses.
PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). Methods that are available in the package include: parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Input data types include molecular sequences, gene frequencies, restriction sites and fragments, distance matrices, and discrete characters.