Table 5.

Comparison of running time in seconds between HAP and PHASE

	Mean		Standard deviation		Minimum		Maximum
Number of SNPs	HAP	PHASE	HAP	PHASE	HAP	PHASE	HAP	PHASE
10	0.06	19.12	0.03	8.88	0.03	12.08	0.10	37.74
20	0.56	109.71	0.30	68.78	0.23	46.24	1.08	237.78
30	1.10	327.55	0.55	257.59	0.54	99.76	2.24	887.82
40	1.53	833.99	0.61	831.93	0.80	165.57	2.58	2906.84
50	1.99	1643.49	0.75	1454.08	1.02	581.80	3.32	5013.80
60	2.45	3719.40	0.83	4352.68	1.19	915.95	3.74	14554.47
70	3.02	5931.03	0.91	5680.70	1.56	1212.59	4.48	18593.30
80	3.43	8071.75	1.00	7495.58	1.74	1774.35	5.12	26016.98
90	3.82	10585.10	1.10	9307.13	1.90	2167.37	5.72	32363.89
100	4.42	13409.43	1.25	12113.96	2.16	2634.38	6.53	40183.36
110	4.86	16082.93	1.21	12598.09	2.66	6127.91	6.83	44603.33
120	5.25	20283.20	1.20	14935.60	3.31	7756.14	7.14	54431.03
130	5.70	25249.62	1.35	18740.87	3.73	9636.97	8.09	63775.21
140	6.16	30643.41	1.39	18292.52	4.19	12226.41	8.53	69463.15
150	6.63	35768.83	1.46	20482.31	4.79	14280.62	9.05	74459.95
160	7.05	42161.60	1.49	23714.27	5.29	19106.80	9.73	91346.27
170	7.53	51597.25	1.59	30670.41	5.44	20676.32	10.4	113281.51
180	8.09	63743.02	1.72	37621.29	5.72	31889.18	11.08	138096.67

The running time is measured by running both methods from 10 different positions in chromosome 19, with different length of genotypes. Intel Xeon 3.20 GHz CPU is used in the measurement.