Figure 3. Overlap of MSTs and correspondence scores.

Different inner trees specific of residues A and B at positions i and j and their corresponding correspondence scores. White squares identify nodes of (leaves excluded) and black squares identify nodes of . White and black squares identify common nodes between and . The first two trees illustrate perfect inclusion and exclusion. The last two trees illustrate intermediate cases where the number of sequences with residues A and B are equal but correspondence scores are different due to a different distribution of sequences in the tree.