  The primitive data for deducing the Miyazawa-Jernigan contact energy or
BLOSUM score metrix are the pair frequency counts. Each amino acid corresponds
to a distribution. Taking the Kullback-Leibler distance of two probability
distributions as resemblance coefficient and relating cluster to mixed
population, we perform cluster analysis of amino acids based on the frequecy
counts data. Furthermore, Ward's clustering is also obtained by adopting the
average score as an objective function. An ordinal cophenetic is introduced to
compare results from different clustering methods.
