Table 4.

Elapsed-time comparison (in seconds) for algorithms cNW, hSW, and saCSCr

Dataset $<\mathit{\alpha },\mathit{\gamma },\mathit{\theta },\mathit{\kappa },\mathit{\omega }>$	cNW	hSW	saCSCr
<12, 2500, 0.05, 0.06, 0.04>	10,139.36	72.43	6.90
<12, 2500, 0.20, 0.06, 0.04>	9888.84	80.91	6.57
<12, 2500, 0.35, 0.06, 0.04>	10,052.33	80.16	6.28
<25, 2500, 0.05, 0.06, 0.04>	46,311.85	369.02	27.61
<25, 2500, 0.20, 0.06, 0.04>	46,230.07	375.41	28.92
<25, 2500, 0.35, 0.06, 0.04>	46,289.99	400.30	30.44
<50, 2500, 0.05, 0.06, 0.04>	122,165.95	1563.96	125.63
<50, 2500, 0.20, 0.06, 0.04>	121,810.69	1617.89	123.12
<50, 2500, 0.35, 0.06, 0.04>	120,679.32	1662.82	123.77

The number of sequences in the dataset is denoted by $\mathit{\alpha }$; $\mathit{\gamma }$ denotes their lengths; $\mathit{\theta }$ denotes the substitution rate; $\mathit{\kappa }$ and $\mathit{\omega }$ denote the relative insertion and deletion rates, respectively