MrBayes A tool to help you with your Bayesian estimation of phylogeny.
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MrBayes Description

MrBayes is a simple, easy to use application specially designed for the Bayesian estimation of phylogeny. The program takes as input a character matrix in a NEXUS file format. The output is several files with the parameters that were sampled by the MCMC algorithm. MrBayes can summarize the information in these files for the user. Main features: A common command-line interface for Macintosh, Windows, and UNIX operating systems; Extensive help available via the command line; Ability to analyze nucleotide, amino acid, restriction site, and morphological data; Mixing of data types, such as molecular and morphological characters, in a single analysis; A general method for assigning parameters across data partitions; An abundance of evolutionary models, including 4 X 4, doublet, and codon models for nucleotide data and many of the standard rate matrices for amino acid data; Estimation of positively.selected sites in a fully hierarchical Bayes framework.

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