In aligning two protein sequences, some method must be used to score the alignment of one residue against another.
Substitution matrices contain such values.
The late Margaret Dayhoff was a pioneer in protein databasing and comparison. She and her coworkers developed a model of protein evolution which resulted in the development of a set of widely used substitution matrices . Derived from global alignments of closely related sequences. Matrices for greater evolutionary distances are extrapolated from those for lesser ones. Several later groups have attempted to extend Dayhoff's methodology or re-apply her analysis using later databases with more examples.