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.
Here are some key features of "MrBayes":
· 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.