# Substitution matrix

### From Bioinformatics.Org Wiki

PAM and BLOSUM methods are used to estimate the target frequencies and thus the log-odds scores of a substitution matrix:

Sij = log[qij / (pi * pj)] qij = target frequency: change in amino acid from i to j pi, pj = relative frequencies of change

Which are then used to determine the relative probabilities of matches and mismatches.