Download PhyML with empirical profile mixture models
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 akgorithm.
Download PhyloBayes with empirical profile mixture models
To run the MCMC sampler under profile models, use "-catfix cX" option, where X = 20,30, ... 60. For instance
./pb -d dataset -catfix c50 name
will run a mcmc, and store the results in files prefixed with
. For more details, see enclosed pdf manual.