Hello,

I wanted to find out whether DEPS in datamonkey is appropriate for finding evidence of directional selection   in domestic pig populations (comprising different breeds) or in livestock in general.  My observation is that DEPS has been used mostly on viruses. Also I tried DEPS on my pig population and got this warning: Protein model selection identified HIV (within host) + F as the best fit model using cAIC, whereas HIV(between hosts) was used for DEPS analysis.  However of all the models listed in DEPS datamonkey there is none called "HIV (within host) + F" that can be chosen for analysis.  Is there some other place in datamonkey where this model can be found?  Thank you.   

Hi KDO,

You should be able to use DEPS (or a faster version of it called FADE) for ANY set of sequences; there is nothing limiting it only to viral sequence analysis.
You can also ignore the warning about the +F part for DEPS analyses -- the frequencies are always estimated by ML, so the warning is not really applicable.

Sergei

Thanks for the clarification