Table 1. Comparison of algorithms on HomFam.

Algorithm	93 ≤ k ≤ 3000			3000 < k ≤ 10000			10000 < k ≤ 50157			All
	41 families			33 families			18 families			92 families
	SP	TC	time	SP	TC	time	SP	TC	time	SP	TC	time
FAMSA	83.2	64.3	34	88.3	71.3	2:36	79.4	56.9	8:25	84.3	65.4	11:35
Clustal-iter2	86.3	71.5	2:14:18	85.0	68.9	14:33:00	69.5	48.3	34:50:54	82.5	66.0	51:38:12
Clustal-default	85.7	70.8	27:02	82.7	63.9	2:24:36	67.6	46.4	5:51:10	81.1	63.6	8:42:50
MAFFT-default	81.9	64.0	2:15	80.8	57.6	23:55	69.1	46.2	2:05:52	79.0	58.2	2:32:02
MAFFT-parttree	77.0	55.2	2:43	72.4	46.6	15:38	58.0	33.0	43:08	71.6	47.8	1:01:29
MAFFT-dpparttree	80.3	61.2	10:40	79.0	54.5	57:41	63.5	37.8	1:57:02	76.5	54.2	3:05:23
UPP	79.8	62.0	2:58:50	81.8	64.3	6:45:21	61.9	42.2	6:48:59	77.0	59.0	16:33:10
Kalign-LCS	79.8	61.3	4:17	80.6	57.6	1:31:45	67.9	44.4	64:23:14	77.8	56.7	65:59:16
Kalign2	77.4	56.2	7:04	77.6	57.1	2:30:45	64.8	41.6	97:48:46	75.0	53.7	100:26:35
MUSCLE-default	72.0	53.2	35:35:44	—	—	—	—	—	—	—	—	—
MUSCLE-maxiters2	71.8	51.4	12:35	67.1	41.6	2:27:51	40.6	21.6	30:35:03	68.8	42.1	33:15:29