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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 1.1.2 posted March 13, 2009
This is a bug-fix release. Please replace version 1.1 or version 1.1.1 with this version to avoid the use of possibly incorrect likelihoods under invariant sites models or (for any model) trees with more than 26 taxa (see description of the "underflow" bug in BUGS file for details).
Phycas version 1.1.2 can be downloaded for Windows or Mac on the Download page. (Linux versions are available but must be compiled from the C++ sources.)