Dear Sergei, I have performed some FEL and IFEL tests in datamonkey. I found several sites as being under positive selection. For example: 24 under FEL and 13 under IFEL analyses (the sample has 14 sequences and 786 segregating sites). Only 6 sites coincide in both analyses. I read your 2006 plos paper about differential selection and have a couple of questions about my results:

1) the sites only detected by FEL can be considered transient substitutions?

2) Sites detected by IFEL should be detected by FEL?

3) Should I need to do some more test or is the comparison between FEL and IFEL enough?


thank you very much!!
and sorry if I am making questions already treated in other posts!

,
Antonio

Ok, Sergei thank you very much for your answer.

Concerning point 3 I am comparing several populations, I have completed the study with a GA branch analysis. I think that if I want to test for different adaptation in different populations I have to use the Hyphy package and redone the ifel analysis plus the population level adaptation test. Is this right?
thank you very much for all your help!

,
Antonio