BEAST, Bayesian Evolutionary Analysis Sampling Trees, is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. The program is orientated towards (strict and relaxed) molecular clock analyses...
FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. As with most of my programs, it was written for my own needs so may not be as polished and feature-complete as a commercial program...
WARNING: Se-Al will not run on Mac OS X 10.7
Due to the lack of support for older PPC code (via the 'Rosetta' system present in older versions)...
Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process...
TempEst is a tool for investigating the temporal signal and 'clocklikeness' of molecular phylogenies. It can read and analyse contemporaneous trees (where all sequences have been collected at the same time) and dated-tip trees (where sequences have been collected at different dates)...
Tracer is a program for analysing the trace files generated by Bayesian MCMC runs (that is, the continuous parameter values sampled from the chain). It can be used to analyse runs of BEAST, MrBayes, LAMARC and possibly other MCMC programs.
Although Tracer can be used with programs other than BEAST, users are strongly advised to join the BEAST mailing-list...
