Table 3.

Average rank scores for the different methods on simulated datasets, using the accuracy metrics described in the main text and in Table 2

	Low indel rate			Medium indel rate			High indel rate
	α C	${\alpha }_{C^{+}}$	AMA	α C	${\alpha }_{C^{+}}$	AMA	α C	${\alpha }_{C^{+}}$	AMA
MinRisk (C), g=0	0.91	0.89	0.90	0.96	0.92	0.93	0.89	0.88	0.88
MinRisk (C), g=0.5	0.89	0.73	0.84	0.93	0.50	0.78	0.84	0.09	0.40
MinRisk (C), g=1	0.88	0.63	0.80	0.90	0.30	0.65	0.79	0.03	0.28
MinRisk (C +), g=0	0.86	0.98	0.96	0.87	1.00	1.00	0.76	1.00	1.00
MinRisk (C +), g=0.5	0.89	0.92	0.92	0.93	0.94	0.94	0.86	0.94	0.94
MinRisk (C +), g=1	0.89	0.84	0.88	0.91	0.74	0.85	0.83	0.34	0.55
MergeAlign	0.65	0.40	0.48	0.80	0.46	0.58	0.73	0.36	0.45
S-Coffee	0.08	0.02	0.10	0.15	0.01	0.10	0.29	0.00	0.04

Highest values for each column shown in bold.