Table 1

Comparison of scoring methods
Scoring method % negative components
Difference Square root 0
Difference 3.2
Dissimilarity BLOSUM30 4.1
BLOSUM45 3.5
BLOSUM62 3.6
BLOSUM80 3.5
PAM40 4.3
PAM80 4.8
PAM120 5.1
PAM160 5.6
PAM250 6.3
GONNET 3.5
JTT 6.5
JTT_TM 6.7
PHAT 4.1

The percent of negative components represents the weight of negative components in the variance of the data.

Pelé et al.

Pelé et al. BMC Bioinformatics 2012 13:133   doi:10.1186/1471-2105-13-133

Open Data