Substitution Matrices
	• Log-odds frequency of amino acid substitution in conserved proteins • PAM (point accepted mutation) series was developed by Margaret Dayhoff in the 1970’s – Based on a small number of highly conserved proteins and extrapolated over different evolutionary distances • The BLOSUM (blocks substitution matrix) series was developed by Steve and Jorja Henikoff at FHCRC – Based on observed substitution frequencies in more than 2000 conserved blocks found in families of related proteins