amino acid substitution matrix WS annotations Group, UGA A scoring matrix that describes the probability at which one amino acid in a protein sequence changes to other amino acid over time. There are two options for the protein weight matrix: BLOSUM and PAM. The actual matrix that is used depends on how similar the sequences to be aligned at this alignment step are. Different matrices work differently at each evolutionary distance. http://en.wikipedia.org/wiki/Substitution_matrix scoring matrix