Bayesian Analysis in Molecular Biology and Evolution (BAMBE) is a free software package for the Bayesian analysis of phylogenies. The package includes programs for analyzing aligned DNA or RNA sequence data and allows data sets with gaps or indeterminate sites. The main program uses a variety of Metropolis-Hastings algorithms to sample from the joint posterior distribution of phylogenetic trees and likelihood model parameters. Other programs in the distribution help in analysis of the sampled trees and parameter values.
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