Homology search

Smith-Waterman

BLOSUM62 or BLOSUM50

Higher numbers in the PAM matrix naming scheme denote larger evolutionary distance, while larger numbers in the BLOSUM matrix naming scheme denote higher sequence similarity and therefore smaller evolutionary distance. Example: PAM150 is used for more distant sequences than PAM100; BLOSUM62 is used for closer sequences than BLOSUM50.

[Hulsen2006b] recommends using SSEARCH with e-values for doing pairwise sequence comparison.