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Bayesian Evolutionary Analysis Sampling Trees (BEAST) is a program for Bayesian Markov Chain Monte Carlo (MCMC) analysis of molecular sequences. It is oriented towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST averages over tree space, so that each tree is weighted proportional to its posterior probability.

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Additional Information: 

Lemey P, Rambaut A, Drummond AJ & Suchard MA (2009) PLoS Computational Biology 5, e1000520.
Drummond AJ & Rambaut A (2007) "BEAST: Bayesian evolutionary analysis by sampling trees." BMC Evolutionary Biology 7, 214.
Drummond AJ, Nicholls GK, Rodrigo AG & Solomon W (2002) Genetics 161, 1307-1320.

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