What is the best way to apply the +G/gamma models in the codeml (PAML) control file please? And what should these be set to when the model is not +G/gamma?
My adviser previously suggested the following (but that was when we thought we could apply +I or+I+G models, which codeml does not).
When the model includes G: fix_alpha = 0 alpha = 0.5 nCatG = 4
When the model does not include G: fix_alpha = 1 alpha = 0 (assuming nCatG is ignored in this case)
Thanks for your help! Danielle.