Table 1 Comparison of scoring methods
From: Bios2mds: an R package for comparing orthologous protein families by metric multidimensional scaling
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 | |