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Figure 1 | Algorithms for Molecular Biology

Figure 1

From: A new, fast algorithm for detecting protein coevolution using maximum compatible cliques

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.

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