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Firstly, Bayesian methods allow the relatively straightforward implementation of extremely complex evolutionary models.
Secondly, there is an often erroneous perception that Bayesian estimation is "faster" than heuristic optimization based on a maximum likelihood criterion.
Bayesian Markov chain Monte Carlo (MCMC) has already been enthusiastically embraced as the state-of-the-art method for phylogenetic reconstruction, largely driven by the rapid and widespread adoption of Mr Bayes .
One of the most promising recent advances in molecular phylogenetics has been the introduction of relaxed molecular clock models that do not assume a constant rate across lineages [13–20].
For example, consider the analysis of a multiple sequence alignment of coding DNA.
In a BEAST analysis, it is possible to allow each codon position to have a different substitution rate, a different amount of rate heterogeneity among sites, and a different amount of rate heterogeneity among branches, whilst sharing the same intrinsic ratio of transitions to transversions with the other codon positions.
BEAST source code is object-oriented, modular in design and freely available at under the GNU LGPL license.
BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation.