Figure 1.

Two alignments of protein families A and B with proteins from two species, which are indicated by different background colors. Black and red nodes and edges compose the matching graph G. A matching θ is shown in red. A unit of coevolution ((a, b), (a', b')) within θ is highlighted in bold. For this toy example, we have ℓ_A(a, a') = 12 (matches + mismatches), ∆_A(a, a') = 11 (mismatches), ℓ_B (b, b') = 19 and ∆_B (b, b') = 15 and a resulting probability $f\left({\text{Δ}}_A\left(a,a^{\prime }\right),{\text{Δ}}_B\left(b,b^{\prime }\right)\right)=\left(\begin{array}{c}\hfill 12\hfill \\ \hfill 11\hfill \end{array}\right)\left(\begin{array}{c}\hfill 19\hfill \\ \hfill 15\hfill \end{array}\right)/\left(\begin{array}{c}\hfill 31\hfill \\ \hfill 26\hfill \end{array}\right)\approx 0.274$. Note the lower score of the unit ((a', b'), (a", b")), which is $\left(\begin{array}{c}\hfill 12\hfill \\ \hfill 11\hfill \\ \hfill \hfill \end{array}\right)\left(\begin{array}{c}\hfill 19\hfill \\ \hfill 3\hfill \\ \hfill \hfill \end{array}\right)\left./ \right)\left(\begin{array}{c}\hfill 31\hfill \\ \hfill 14\hfill \\ \hfill \hfill \end{array}\right)\approx 4.4\cdot 10^{-5}$.