BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards molecular clock analyses. It is intended not only as a method of constructing phylogenies but also of testing evolutionary hypotheses sampled over probable tree-space...
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...
R script implementing maximum likelihood estimator of the time averaged values of a quantitative trait over a pair of lineages. Useful for comparative studies of substitution rates...
Se-Al is an application for creating multiple sequence alignments from nucleotide and amino acid sequences. At the moment it does not do any automatic alignments but is intended for the production of hand alignments and for preparing input for alignment programs such as CLUSTAL and phylogeny reconstruction programs such as PHYLIP and PAUP...
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...
