Table 3.
Performance of aligners on the PREFAB protein reference alignment benchmark
| Aligner | Overall (1927) | Time |
|---|---|---|
| DIALIGN | 57.2 | 12 h, 25 min |
| CLUSTALW | 58.9 | 2 h, 57 min |
| T-Coffee | 63.6 | 144 h, 51 min |
| MUSCLE | 64.8 | 3 h, 11 min |
| MAFFT | 64.8 | 2 h, 36 min |
| ProbCons | 66.9 | 19 h, 41 min |
| ProbCons-ext | 68.0 | 37 h, 46 min |
Entries show the average Q (equivalent to SP) score achieved by each aligner on all 1927 alignments of the PREFAB database. All scores have been multiplied by 100. Running times for programs over the entire database are given for each program in hours and minutes. The best results in each column are shown in bold.