Figure 1.

Example of coevolution of two protein families. Although MMM makes use of distance matrices, we can illustrate the solution sought by considering the phylogenetic trees of two protein families A and B. The sequences from a3, a4 and a5 would match with the corresponding proteins b3, b4 and b5 by the MMM algorithm because the subtree of those sequences in A is only different from the corresponding subtree in B by a scaling factor in the branch lengths. With a strict tolerance, sequences from species 1 and 2 would not contribute to the match, as the relative branch lengths to the other sequences are very different.