Hi guys~ I have two sets of proteins: let's say A set (contains 100 A genes) and B Set containing (100 B genes). I want to show that genes in A Set are more conserved and less divergent than ones in B Set. I build phylogenetic trees, branch length for A Set is much longer than one from B Set. But it does not seem to be a good way to compare. I also tried network analysis using protein sequence identity, most genes from A set form a big network however genes from B set forms multiple network at the same cut value.
Could someone know a better way to compare using a more quantitive way?