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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.
