SIMMAP is a post tree analysis GUI software package for stochastically mapping mutations on phylogenies.SIMMAPimplements stochastic mutational mapping using a wide range of models: 4 x 4 general reversible nucleotide models and standard Mk character models. SIMMAP allows addressing a variety of evolutionary questions. Specifically, questions about the number, type and placement of mutations on a phylogeny. In addition, tests of character correlation, positive selection, and ancestral states are available.
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SIMMAP: stochastic character mapping of discrete traits on phylogenies.
BMC Bioinformatics. 2006 Feb 23;7:88.