Table 6. Q scores and CPU times on SABmark.
| Method | All | Superfamily | Twilight | CPU |
|---|---|---|---|---|
| MUSCLE | 0.430 | 0.523 | 0.249 | 1886 |
| T-Coffee | 0.424 | 0.519 | 0.237 | 5615 |
| MUSCLE-p | 0.416 | 0.511 | 0.230 | 304 |
| NWNSI | 0.410 | 0.506 | 0.223 | 629 |
| CLUSTALW | 0.404 | 0.498 | 0.220 | 206 |
| FFSNT1 | 0.373 | 0.467 | 0.190 | 75 |
| Align-m | 0.348 | 0.445 | 0.172 | 8902 |
All gives the average Q score over all SABmark alignments, Superfamily and Twilight are average Q scores on the two subsets. These are computed first by averaging Q for each pair in a single multiple alignment, then averaging over multiple alignments. This corrects for the lack of independence between pairs in a given multiple alignment. Align-m aborted in nine cases; quoted averages for this program are for completed alignments. Selected P-values are: MUSCLE > T-Coffee P = 0.14, MUSCLE > MUSCLE-p P = 4×10–5, MUSCLE > NWNSI P = 6 × 10–6, MUSCLE-p > NWNSI P = 0.03, T-Coffee > MUSCLE-p P = 0.1, T-Coffee > Align-m P < 10–10.