For each branch in the phylogenetic trees of the protein families, the number of mismatches that were observed were recorded and a record kept of the two amino acids involved.[1] These counts were used as entries below the main diagonal of the matrix A {\displaystyle A} . Since the vast majority of protein samples come from organisms that are alive today (extant species), the 'direction' of a mutation cannot be determined. That is, the amino acid present before the mutation cannot be distinguished from the amino acid that replaced it after the mutation.