This simplified description hides subtle details that are important in the
construction of scoring matrices. The probability of Ser mutating into Phe
in proteins that diverged 15million years ago (e.g., related proteins in mouse
and rat) is smaller than the probability of the Ser ! Phe mutation in proteins
that diverged 80 million years ago (e.g., related proteins in mouse and
human). This observation implies that the best scoring matrices to compare
two proteins depends on how similar these organisms are.