Substitution matrix for likelihood calculation?

[jba462]

Is there a way to specify a substitution matrix when calculating the likelihood of a tree? I am using amino acid data as a test set and would like to include a model of evolution in the calculation. I am assuming that, by default, Pylogeny uses a "Poisson" model or something similar to Jukes-Cantor. I would like to evaluate likelihoods using WAG, LG, JTT and even some custom matrices. Moreover, I'd like to apply separate models to each alignment site where appropriate.

Is this possible in Pylogeny? If not, is this functionality slated for future releases?

Thanks!