Method | ROSE | RNASim | Indelible | ROSE | CRW | 10 AA | HomFam | HomFam |
|---|
| Â | NT | 10K | 10K | AA | Â | Â | (17) | (2) |
|---|
UPP | 0.6 | 6.7 | 6.7 | 0.2 | 11.6 | <0.1 | 1.3 | 0.5 |
PASTA | 0.6 | 3.9 | 1.3 | 0.2 | 3.2 | 0.2 | 1.5 | 1.3 |
MAFFT | 0.4 | 0.1 | 1.4 | <0.1 | 0.4 | 0.1 | <0.1 | 0.1 |
Muscle | 0.5 | 0.8 | 1.2 | <0.1 | 5.9 | 0.2 | 1.3 | X |
Clustal | 0.4 | 4.8 | X | 0.1 | 2.8 | <0.1 | 0.3 | 0.3 |
- Average wall-clock running time for the full-length datasets for which most methods could complete; this includes everything other than the RNASim datasets with 50,000 or more sequences. UPP is run in default mode. Results marked with an X indicate that the method failed to terminate within the time limit (24 hours on a 12-core machine). All methods but Muscle had parallel implementations and were able to take advantage of the 12 cores. Muscle failed to align two of the HomFam datasets; we report separate average results for the 17 HomFam datasets for all methods and the two HomFam datasets for all but Muscle.
