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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.
Phycas is still in development and should be considered alpha software. Unless you are a bit adventurous, you might want to wait a bit before trying it. We plan to have an official release ready by August, 2008.