ProtTest and PhyML

Question

[Michel Edwar]

I am drawing a phylogenetic tree. To select the most appropriate model, I ran ProtTest with the aligned amino acid sequences. The ProtTest suggested that the best models for the two LG+I+G+F. However, When I try to build the trees using PhyML, I do not know how to set the parameters to fit to the suggested models. The option -m (or --model) can accept LG. But, which options can accept G , I and F in the suggested models?

Answer 1

[h.mon]

See How To Set The Substitution Model In Phyml? and here.