| Algorithm . | All . | 90% fastest . | 99% fastest . | 1% slowest . |
|---|---|---|---|---|
| DP | 833.3 s | 133.5 s (16.0%) | 437.9 s (52.6%) | 395.4 s (47.4%) |
| Sparse DP | 75.3 s | 13.9 s (18.5%) | 33.9 s (45.0%) | 41.4 s (55.0%) |
| Speed up | 11-fold | 10-fold | 13-fold | 10-fold |
| Algorithm . | All . | 90% fastest . | 99% fastest . | 1% slowest . |
|---|---|---|---|---|
| DP | 833.3 s | 133.5 s (16.0%) | 437.9 s (52.6%) | 395.4 s (47.4%) |
| Sparse DP | 75.3 s | 13.9 s (18.5%) | 33.9 s (45.0%) | 41.4 s (55.0%) |
| Speed up | 11-fold | 10-fold | 13-fold | 10-fold |
We report running times in seconds and as fractions of the total running time for all instances (5151 alignments). We also report running time for the 90 and 99% fastest and for the 1% slowest alignments. For both algorithms, instances were sorted separately.
| Algorithm . | All . | 90% fastest . | 99% fastest . | 1% slowest . |
|---|---|---|---|---|
| DP | 833.3 s | 133.5 s (16.0%) | 437.9 s (52.6%) | 395.4 s (47.4%) |
| Sparse DP | 75.3 s | 13.9 s (18.5%) | 33.9 s (45.0%) | 41.4 s (55.0%) |
| Speed up | 11-fold | 10-fold | 13-fold | 10-fold |
| Algorithm . | All . | 90% fastest . | 99% fastest . | 1% slowest . |
|---|---|---|---|---|
| DP | 833.3 s | 133.5 s (16.0%) | 437.9 s (52.6%) | 395.4 s (47.4%) |
| Sparse DP | 75.3 s | 13.9 s (18.5%) | 33.9 s (45.0%) | 41.4 s (55.0%) |
| Speed up | 11-fold | 10-fold | 13-fold | 10-fold |
We report running times in seconds and as fractions of the total running time for all instances (5151 alignments). We also report running time for the 90 and 99% fastest and for the 1% slowest alignments. For both algorithms, instances were sorted separately.
This PDF is available to Subscribers Only
View Article Abstract & Purchase OptionsFor full access to this pdf, sign in to an existing account, or purchase an annual subscription.
