I ran Prottest to determine the best model for a given protein sequence alignment, so I can eventually use that model in RAxML. The output of Prottest tells me that the best model according to AIC is: WAG+I+G+F.
Now I have to set the model in RAxML command. Based on the RAxML manual I think "WAG" is the model, "I" is for invariant sites, "F" is for using empirical AA frequency, but i'm not sure what the "G" is for? This is what I have come up with, does anyone know if this is the right model based on the Prottest output?
raxmlHPC-PTHREADS-SSE3 -m PROTGAMMAIWAGF