BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards molecular clock analyses. Although it can be used as a method of constructing phylogenies it is particularly intended for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. It uses a complex input format that allows the user to design and run a large range of models. We also include a program that can convert NEXUS files into this format.