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CPU times. The total CPU time required to create all alignments in each test set, measured in seconds on a 2.5 GHz Pentium 4 desktop computer.
| Method | PREFAB | BAliBASE | SABmark | SMART |
| MUSCLE-fast | 540 | 11 | 45 | 30 |
| FFTNS1 | 720 | 16 | 70 | 46 |
| MUSCLE-prog | 3,000 | 52 | 429 | 180 |
| MUSCLE | 11,000 | 81 | 1,500 | 560 |
| POA-blast | 11,000 | 90 | 290 | 670 |
| CLUSTALW | 15,000 | 160 | 210 | 480 |
| POA | 24,000 | 130 | 380 | 880 |
