Figure 2
From: Evolutionary models for insertions and deletions in a probabilistic modeling framework
Regularized rate matrix generated from BLOSUM62 Regularized rate matrix generated from BLOSUM62 after the QOG algorithm has been applied. The matrix has been rescaled to have an average number of one substitution per amino acid. In this simple case in which there was at most one negative off-diagonal entry per row, the regularization process requires the negative off-diagonal value to be set to zero (represented in bold in this Figure), and to shift the rest of the elements in that row by the corresponding amount so that the sum of all elements is zero. Rows without any off-diagonal negative values remain unchanged from the values obtained in Figure 1.