CAT : Empirical profile mixture models for phylogenetic reconstruction.

Le S.Q., Gascuel O., Lartillot N. Bioinformatics. 2008 Oct 15;24(20):2317-23.

Please cite THESE papers if you use CAT.

Download PhyML with empirical profile mixture models

Click here to download PhyML-CAT.

To set the amino-acid replacement model equal to one of the available profile mixtures, use the "-c20", "-c30", ... "-c50" options. For instance : 
    ./phyml -d aa -m C20 -i dataset -c 4 -b 0 -s SPR
here, you combine the C20 model (profile mixture with 20 categories) with a discretised gamma distribution (4 bins), and using the SPR heuristic search algorithm.

© Copyright 2008 by Le Si Quang, Olivier Gascuel and Nicolas Lartillot.

The software is provided "as is" without warranty of any kind. In no event shall the author be held responsible for any damage resulting from the use of this software, including but not limited to the frustration that you may experience in using the package. The packages, including source codes, example data sets, executables, and the user's guide, are distributed free of charge for academic use only.