Table 2.

Running times for the Hill dataset

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.