Table 4.
Crumble results for 90 kb of genomic DNA from seven species.
| Time | Log-likelihood1 | ||
|---|---|---|---|
| Pecan2 | 11.3 | -0.354 | |
| Crumble w/Pecan | 60% | 7.42 | -0.355 |
| 30% | 4.67 | -0.357 | |
| 15% | 5.42 | -0.357 | |
| FSA3 | 38.3 | -0.374 | |
| Crumble w/FSA | 60% | 20.4 | -0.375 |
| 30% | 12.2 | -0.375 | |
| 15% | 9.68 | -0.376 | |
| MUSCLE4 | _a | _a | |
| Crumble w/MUSCLE | 60% | _a | _a |
| 30% | 153. | -0.363 | |
| 15% | 59.2 | -0.367 | |
1 The log-likelihood of the alignment as calculated by phyloFit, in millions of nats.
2 Pecan was run with default parameters.
3 FSA was run with the --exonerate, --anchored, --softmasked, and --fast flags.
4 MUSCLE was run with default parameters.
5 This problem was unable to be aligned due to running out of memory.
The run-time and log-likelihood score of Crumble alignments. Each underlying alignment method (Pecan, FSA, MUSCLE) was tested on the dataset. Crumble was then used to break the problem into sub-problems that were approximately 60%, 30%, and 15% of the length of the original problem. While MUSCLE was unable to align this problem directly, using Crumble we were able to apply it to this problem.