Dear Sergei,

Recently, I submitted a paper about evolution. I used REL to investigate the positive selection.

One reviewer asked me "Were models implementing variable dS ratios also run? Were there any difference in terms of results?"

So I have a question: How to run the models implementing variables dS ratios?

I would like to introduce how I use Datamonkey, maybe I miss something:
When I run Datamonkey, I usually execute an automatic model selection tool to find the best modle first, then according to the selestion results, I set the nucleotide substitution bias model (AC, CT, CG...something like that), then run the analysis, finally get the results.
Is this process right?

Thank you very much!
Best regards,

Sundy

Dear Sundy,

SLAC, FEL, REL and PARRIS on datamonkey all include variable dS AND dN, so you should be all set. Automatic model selection only pertains to the nucleotide component of the model and has no effect on how dS and dN are modeled.

HTH,
Sergei

Dear Sergei,

Thank you very much!
I got it.
Best,

Sundy