Fig. 1

Example of Potts model representing a MSA of length 4. Each column in the MSA is associated with a field vector \(v_i\) of length \(q=20\) where each \(v_i(a)\) is a real value weighting positively or negatively the occurrence of letter a at position i. Each pair of positions (i, j) is associated with a \(q \times q\) coupling matrix \(w_{ij}\) where \(w_{ij}(a,b)\) are real values weighting positively or negatively the co-occurrence of letters a and b respectively at position i and j