Hi,

Very easy (and maybe stupid) question..  ;)
I would like to apply an amino acid substitution model considering the frequencies of the model (so with +F). So, in the the folder "TemplateModels" we can find 2 batch files for each model like "WAG.mdl" and "WAG_F.mdl". Initially, "WAG_F.mdl" should consider the frequencies (because the name of the batch file..) but when I go into the script it seems that the frequencies are applied in "WAG_F.mdl" (where "equalFreqs" introduces a particular frequency for each amino acid state at the end of the script).
So, to consider +F which batch file should I use ("WAG.mdl" or "WAG_F.mdl")?.

Many thanks!   :)

Best,
Miguel