Hi there,

1). Generally, MEME will be much more powerful than iFEL: for example the latter will only detect selection if ON AVERAGE omega > 1 on all internal branches. Hence you are likely to miss episodic selection.

2). It is possible that in some of the species, selection is not fully resolved; however since in this case they are starting with the same allele, it is likely that you are simply not picking up some adaptive change because it has not yet occurred.

3). iFEL was originally designed to deal with situations where there is a lot of variation in terminal lineages (e.g. individual viral isolates), which has not been passed through the selection filter (e.g. due to onward viral transmission). In that case, it may be possible to mistake neutral variation (or something beneficial only to a single host, but deleterious on average, e.g. a rare CTL allele escape) for selection.

My advice would be to just run MEME.

Sergei