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BEAST, Bayesian Evolutionary Analysis Sampling Trees, is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is orientated towards (strict and relaxed) molecular clock analyses. It can be used as a method of constructing phylogenies, but it is also 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 an XML 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.