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From Phycas
Phycas is a Python application for carrying out phylogenetic analyses. Phycas is also a C++ and Python library that can be used to create new applications or to extend the current functionality.
New version 1.1 posted February 11, 2009
Two new commands (ps and sump) are included in this release. The ps command implements path sampling (a.k.a. thermodynamic integration) and a new method steppingstone sampling, both of which are used to estimating marginal likelihoods for models (the Bayes factor used to compare models is a ratio of marginal likelihoods). The sump command is analogous to the command of the same name in MrBayes.
Phycas version 1.1 can be downloaded for Windows or Mac on the Download page. (Linux versions are available but must be compiled from the C++ sources.)
