Table 1.

Comparison of log-affine and affine gap costs

Lengths	Log-affine			Affine
	Speed	Scaled	Quality	Speed	Scaled	Quality
1600 × 1600	570	100	72%	211	37	58%
1600 × 800	285	50	78%	110	19	68%
800 × 800	147	26	69%	58	10	57%
800 × 400	76	13	76%	32	5.6	67%
400 × 400	41	7.1	64%	18	3.2	56%

Sets of 1000 simulated sequence pairs were aligned holistically using a match cost of 0, a mismatch cost of 1 and a gap cost of either w_k = 1.67884 + 0.279091 k + 1.06161 ln k or w_k = 6.86637 + 0.281073 k. Speed is the number of seconds Ngila spent aligning the sets, averaged across four runs. Quality is calculated by the average identity of Ngila’s alignments to the simulated alignments (Cartwright, 2006). Tests were done on a 3GHZ Xeon workstation.