Substitution matrices are among the most widely used scoring techniques: BLAST, Phylip and other alignment packages, all use them. However these matrices are general, ignore organism specific properties, and do not provide customized scoring schemes. We present a phage specific Blosum matrix based on the abundances of aligned substitutions. These matrices use information from approximately five and a half million significantly similar protein alignments and over five hundred phage genomes. Our scoring matrix is significantly different from the existing PAM and BLOSUM matrices and indicate the need for similar treatments for other groups of organisms.