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 2.0 coming soon...
July 10, 2012: Version 2.0 is nearing completion and will feature a diversity of Bayesian model selection methods, including marginal likelihood estimation methods (thermodynamic integration, generalized stepping-stone, and inflated density ratio) as well as two posterior predictive methods (Gelfand-Ghosh and Conditional Predictive Ordinates). Coding has been completed and we are currently testing the newer methods.
New version 1.2.0 posted August 9, 2010
Phycas version 1.2.0 can be downloaded for Windows or Mac on the Download page. (Linux versions are also available but must be compiled from the C++ sources.) New features include support for data partitioning and the generalized stepping stone method for estimating marginal likelihoods.