Table 4.
Results for the ultra-large datasets
| Family | Method | SP | TC | Hours | Expansion |
|---|---|---|---|---|---|
| PF00005 | learnMSA | 74.9 | 22.2 | 10.0 | 1.89 |
| UPP | 73.5 | 10.2 | 52.5 | 1.98 | |
| MAFFT | error | ||||
| MAGUS | timeout | ||||
| Regressive T-Coffee | error | ||||
| PF07690 | learnMSA | 56.1 | 0.0 | 30.2 | 1.82 |
| UPP | 51.6 | 0.0 | 35.5 | 2.48 | |
| MAFFT | error | ||||
| MAGUS | timeout | ||||
| Regressive T-Coffee | error | ||||
| PF00096 | learnMSA | 92.9 | 6.5 | 0.9 | 1.16 |
| UPP | 86.3 | 0.0 | 1.7 | 2.23 | |
| MAFFT | 84.1 | 16.1 | 0.3 | 2.74 | |
| MAGUS | 94.8 | 3.2 | 3.6 | 4.68 | |
| Regressive T-Coffee | 69.9 | 0.0 | 0.9 | 6.55 | |
| PF00072 | learnMSA | 92.4 | 39.2 | 2.9 | 1.1 |
| UPP | 91.4 | 34.6 | 6.7 | 1.32 | |
| MAFFT | 64.9 | 4.6 | 7.6 | 3.69 | |
| MAGUS | 85.8 | 33.1 | 24.8 | 2.41 | |
| Regressive T-Coffee | output too large | ||||
| PF00400 | learnMSA | 18.0 | 0.0 | 1.1 | 1.29 |
| UPP | 3.6 | 0.0 | 2.0 | 2.62 | |
| MAFFT | 0.0 | 0.0 | 2.3 | 7.71 | |
| MAGUS | 6.9 | 0.0 | 12.6 | 17.32 | |
| Regressive T-Coffee | 0.0 | 0.0 | 2.0 | 51.28 | |
| PF00069 | learnMSA | 83.4 | 24.9 | 11.3 | 1.37 |
| UPP | 83.3 | 20.2 | 19.5 | 1.6 | |
| MAFFT | 54.9 | 5.4 | 53.0 | 3.52 | |
| MAGUS | 65.4 | 18.1 | 29.1 | 4.77 | |
| Regressive T-Coffee | error | ||||
| PF12796 | learnMSA | 72.4 | 0.0 | 1.3 | 0.85 |
| UPP | 40.8 | 0.0 | 4.3 | 3.18 | |
| MAFFT | 40.4 | 0.4 | 7.5 | 6.36 | |
| MAGUS | 58.9 | 0.0 | 67.2 | 5.62 | |
| Regressive T-Coffee | output too large | ||||
| PF13855 | learnMSA | 94.7 | 26.2 | 0.8 | 1.05 |
| UPP | 91.0 | 21.5 | 2.5 | 1.71 | |
| MAFFT | 80.6 | 3.1 | 1.2 | 3.05 | |
| MAGUS | 94.7 | 38.5 | 54.1 | 1.47 | |
| Regressive T-Coffee | 49.2 | 0.0 | 0.8 | 7.21 | |
| PF00041 | learnMSA | 79.1 | 16.5 | 1.0 | 1.34 |
| UPP | 74.9 | 22.0 | 2.3 | 2.18 | |
| MAFFT | 43.2 | 0.0 | 2.0 | 7.83 | |
| MAGUS | 72.6 | 10.1 | 53.8 | 6.4 | |
| Regressive T-Coffee | 37.0 | 0.0 | 0.8 | 15.16 | |
| PF07679 | learnMSA | 94.1 | 50.0 | 0.9 | 1.11 |
| UPP | 88.7 | 46.0 | 2.9 | 1.43 | |
| MAFFT | 68.1 | 13.0 | 1.1 | 3.36 | |
| MAGUS | 84.0 | 42.0 | 4.3 | 2.12 | |
| Regressive T-Coffee | 44.2 | 2.0 | 0.6 | 8.55 | |
Expansion denotes the ratio of the length of the predicted alignment (induced by the reference sequences) to the reference alignment length. Values greater than 1 indicate underalignment (i.e., the estimated alignment is longer than the reference). Timeout: the alignment could not be completed by the method within a wall clock limit of 3 days. Error: the alignment failed with an error (either out of memory or another unknown reason). Output too large: the alignment was successful, but the output file was impractically large to be properly postprocessed (e.g., PF12796: T-Coffee 445 GB, learnMSA 1.2 GB). For each cell and column, the best value is in boldface.