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BEAST (Bayesian Evolutionary Analysis Sampling Trees) is a package of programs 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.
Input data file format
XML
Instructions
First format your nexus file using BEAUti, then run BEAST, then analyze your data using Tracer, TreeAnnotator, and FigTree. All programs can be downloaded from the BEAST web site.
On a UNIX operating system, run the following commands:
beauti
beast
tracer
treeannotator
figtree
The BEAST tutorial is found on the faculty page of Andrew Rambaut.
BEAST is available at the BEAST web site and further information regarding the program can be found in the MANUAL.
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