I am trying to figure out how sequences of two protein families are conserved in various species. I have two fasta files containing sequences of each of the families. Now I want to find out in the scale of 0-1 the amino acid conservation of the sequences in the files.
Does it make sense? I am wondering if there is any technical term which relates to what I am trying to do. Is it equivalent to the average of the dN/dS of all amino acid sites? The main objective is to identify if there is any evolutionary pressure which makes one family more conserved than the other.