FIGURE 1 

Illustration of the model used to assign a probability P(D|a) to the joint multiple sequence alignment D of two protein families given an assignment a of interaction partners between them. Sequences from the same genome have the same color and horizontally aligned sequences are assumed to interact. The probabilities of pairs of alignment columns (ij) depend on the number of times n^ij that amino acids () occur in the corresponding columns. A dependence tree T and the corresponding factorization of the probability P(D|a, T) of the entire alignment given the assignment and dependence tree is illustrated at the bottom of the figure.