Figure 1.

CovET Pipeline.A, CovET Equation, ij is a pair of residues, N is the number of sequences in the alignment, n is the division in the tree, g is the group of the tree at division n, v is one of the 17,640 possible nonconcerted variations in a 21 character alphabet, f_ijv is the frequency of nonconcerted variation v in group g. B, vertical dashed lines show division of the tree into groups (blue n = 1, orange n = 2, green n = 6), boxed sequences are resulting groups (g) from each division. C, the substitution matrix for each division in the tree. Instances of nonconcerted variation are shown in different shades of yellow and are used in the penalty function (right). The boxed regions of the matrix represent the pairwise comparison, defined on a per group basis (second substitution matrix has two boxed regions, corresponding to the two groups in the tree at that division). In each box the comparison of the residues in each pair is indicated by the + and - symbols, with + meaning variation and - meaning conservation (i.e., ++ concerted variation, -- conservation, and +- or -+ non-concerted variation).