Maybe I missed something, but I only noticed today that the super-fast likelihood phylogenetics software RAxML can use four different models of sequence evolution.
I seem to remember (?) that it could only do the GTR model. Perhaps they added the three others in a newer version and I missed the change while I was busy using BEAST and otherwise doing non-phylogenetic research? Or did I just never notice before?
Anyway, there is the choice between GTR, JC, K80, and HKY, so the most parameter-rich model, the most parameter-poor, and the two standard models with different rates transitions and transversions. Which is good, because I have a tendency to get GTR or HKY suggested for the data I usually use. It seems, however, as if it is not possible to specify different models for the various parts of the partition.
Anyway, I have accordingly updated the posts on what number of schemes to test in jModelTest and on what models are implemented in the various phylogenetics programs I am familiar with.