Table 2.
Significance test for differences in BAliBASE performance
| Align-M | DIALIGN | CLUSTALW | MAFFT | T-Coffee | MUSCLE | ProbCons | ProbCons-ext | |
|---|---|---|---|---|---|---|---|---|
| Align-M | −(0.61) | −8.2 × 10−6 | −<10−10 | −<10−10 | −<10−10 | −<10−10 | −<10−10 | |
| DIALIGN | −1.9 × 10−5 | −<10−10 | −<10−10 | −<10−10 | −<10−10 | −<10−10 | ||
| CLUSTALW | +2.4 × 10−3 | −1.0 × 10−3 | −3.0 × 10−5 | −4.9 × 10−8 | −6.1 × 10−10 | −<10−10 | ||
| MAFFT | +1.2 × 10−9 | +1.0 × 10−3 | −(0.65) | −1.7 × 10−5 | −2.6 × 10−9 | −4.9 × 10−8 | ||
| T-Coffee | +<10−10 | +8.4 × 10−6 | − (0.92) | −7.0 × 10−3 | −1.5 × 10−6 | −8.4 × 10−6 | ||
| MUSCLE | +<10−10 | +1.9 × 10−8 | +9.6 × 10−6 | +1.7 × 10−3 | −3.0 × 10−3 | −6.6 × 10−3 | ||
| ProbCons | +<10−10 | +<10−10 | +1.6 × 10−7 | +1.9 × 10−6 | +0.012 | +0.043 | ||
| ProbCons-ext | +<10−10 | +<10−10 | +8.3 × 10−6 | +3.2 × 10−5 | +(0.092) | −(0.088) |
Entries show the p-value indicating the significance of a difference in performance between two alignment methods as measured using a Friedman rank test. Nonitalicized values above the diagonal were calculated using SP scores on all alignments, whereas italicized values were computed using CS scores. (+) Method on the left had lower average rank (better performance); (−) Method on the left had higher average rank (worse performance); parentheses denote (nonsignificant) p-values >0.05.