I am trying to identify the amino acids which are under positive selection based on the codon alignment and phylogenetic tree using PAML and SLR. More complex models like M8 or higher seem to have better (closer to 0) log-likelihood compared to M1/M2/M3. Therefore I selected the M8 model.
I also calculated the amino acid residue conservation in each column of the MSA. I expected to obtain dN/dS <1 for conserved sites and dN/dS>1 for the sites which has no conservation. But it turns out that in M8 model the dN/dS is >=1 in rare cases in the completely non-conserved sites. However in M2 all these sites are having dN/dS=1. I am a bit confused as a result.