BEAST (Bayesian Evolutionary Analysis Sampling Trees) is a program for evolutionary inference of molecular sequences designed by Andrew Rambaut and Alexei Drummond (Drummond et al. 2002; 2005; 2006). It is orientated toward rooted, time-measured phylogenies inferred using molecular clock models. It can be used to reconstruct phylogenies and is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses Bayesian MCMC analysis to average over tree space, so that each tree is weighted proportional to its posterior probability.
BEAST is available at the BEAST web site and further information regarding the program can be found in the manual.
BEAST requires infiles to be in the XML format; however, BEAUti will convert NEXUS files into XML for you.
First, format your NEXUS file using BEAUti, then run BEAST. To view and analyze your data use Tracer and TreeAnnotator. LogCombiner is a program to combine log and tree files from multiple runs of BEAST. All four programs can be downloaded from the BEAST web site. Use FigTree to view trees and divergence time estimates.