Table 1.
Compute time required to estimate MSAs of different sizes, measured in seconds
| Size/length | SATCHMO-JS | SATCHMO | ProbCons | T-Coffee | MAFFT |
|---|---|---|---|---|---|
| 100/230 | 30.09 | 198.85 | 85.99 | 219.74 | 2.14 |
| 200/155 | 112.49 | 346.06 | 265.23 | 954.96 | 13.94 |
| 300/126 | 234.79 | 533.97 | 560.93 | 3882.01 | 23.84 |
| 500/392 | 1085.12 | 14 393.87 | 10 469.5 | — | 232.94 |
The first column gives the number of sequences and average sequence length for each dataset. ProbCons and MAFFT were run with five iterations of refinement; SATCHMO, SATCHMO-JS and T-Coffee used default parameters. The time to run SATCHMO-JS includes the time required for MAFFT, QuickTree and the subtree-selection program. MUSCLE’s run-time on these datasets is slightly longer than that of MAFFT (data not shown). T-Coffee failed to complete on the dataset with 500 sequences.