I am using Clustal Omega to align my protein sequences.  That works really well, and I get residues that are conserved.  But it does not calculate the percentage of identical residues.  I tried to use M view. It tells me a percentage number, but that number does not seem to be the percentage of identical residues, because there are 2 proteins clearly share many (not whole a lot) conserved residues, but the percentage is 0.0%