Positively selected sites detected by SLAC, FEL, REL and/or IFEL in HIV-1 and HIV-2 env C2, V3 and C3 regions1.

1PT dataset.Codon – codons selected under 10% level of significance (SLAC, FEL and IFEL) or above a Bayes Factor of 50 (REL) and numbered according to codon env position of HIV-1 HXB2 for HIV-1 dataset or of HIV-2 ALI for HIV-2 dataset. Codons selected simultaneously by SLAC, FEL and REL methods are bold and underlined.SLAC, FEL and IFEL – the first numbers are the dN-dS difference for each site scaled by the total codon tree length, the numbers in parenthesis show P-values for corresponding test of non-synonymous rate being superior to synonymous rate; REL - the first numbers are the expected posterior dN-dS difference for each site scaled to the total codon tree length, the number in parenthesis show the posterior probability of non-synonymous rate being superior to synonymous rate; Bold dN-dS differences correspond to significant P-values or posterior probabilities.