Dear sergei,

Let me see if I understand about IFEL and selection at internal branches.  Look I have a strain which appear positively selected by GA Branch and IFEL, not by SLAC; FEL and REL. Positive selection at internal braches means that during the evolutionary process of this strain it was target of positive selection, that gives to this strain an advantage and then the meaning that these codons positively selected at internal branches not appear at tips means that they are deleterious at long term?

Can you help me to explain it my exam is coming and I have some problems to understand it, the integration of my results.

Thanks

Lauro.

Hi Lauro,

IFEL was designed to test for positive selection at the population level. In a tree of HIV sequences, every interior branch contains at least on transmission event, but terminal branches can contain 0 (i.e. only evolution in one patient). In our PLoS CB 2006 paper, we interpreted positive IFEL results as evidence of long term adaptation (population level), followed by (potentially) deleterious evolution at the tips.

HTH,
Sergei