Figure 1

Mutation matrix generation. A raw mutation matrix is essentially a summary of the counts of all mutations from an amino acid in the reference sequence to every other amino acid in the sequences being compared to the reference. Its normalized equivalent is generated by dividing all the values in the matrix by the highest value found therein. Amino acids in the matrices are always arranged based on a particular physicochemical property. Normalization is done by dividing all entries in the matrix by the highest mutation frequency found in it. For a single alignment, it is possible to generate either one or multiple matrices, depending on the level of analysis that one wishes to subject it to.