Table A3.

Distances for control data set. Median of calculated distances for each reference set of the synthetic control data set (sequence length of 1000 amino acids, no ASRV). Order of methods and values for k are as in Table 1. Note that method B-bin is not listed as it does not calculate distances.

				Reference set of control data
No.	Method		k	1	2	3	4	5	6	7
1	d ML	AA	—	0.7444	1.0993	1.6257	2.0488	2.4290	2.9717	3.3942
2	d PB-ML	CE	—	1.9895	2.4403	2.8530	3.0180	3.0853	3.1345	3.1525
3	d PB-SIM	CE	—	8.6963	9.3471	9.8041	9.9639	10.025	10.063	10.075
4	d PB-ML	AA	—	1.1372	1.5553	1.9732	2.1295	2.1927	2.2274	2.2394
5	d PB-SIM	AA	—	6.8358	7.9676	8.7688	8.9946	9.0815	9.1209	9.1362
6	d ACS	CE	—	1.2536	1.3577	1.4002	1.4128	1.4176	1.4212	1.4226
7	d ACS	AA	—	0.8550	0.9308	0.9668	0.9775	0.9825	0.9856	0.9871
8	d S	CE	5	5.6698	6.1015	6.3468	6.4461	6.4881	6.4606	6.5021
9	d P	CE	5	0.6343	0.8066	0.8821	0.9027	0.9098	0.9157	0.9175
10	d P	AA	4	0.8659	0.9516	0.9778	0.9839	0.9859	0.9870	0.9874
11	d F	CE	5	1.4374	1.7130	1.8759	1.9229	1.9437	1.9578	1.9650
12	d E	AA	4	1850	1946	1978	1986	1990	1994	1992
13	d E	CE	5	1780	1902	1958	1976	1982	1986	1990
14	d F	AA	4	1.7079	2.0017	2.1366	2.1712	2.1889	2.1889	2.1979
15	d S	AA	4	0.2928	0.3099	0.3184	0.3212	0.3230	0.3207	0.3221
16	d LZ	CE	—	0.8560	0.8853	0.8967	0.9002	0.9017	0.9024	0.9029
18	d LZ	AA	—	0.8721	0.8957	0.9045	0.9073	0.9080	0.9086	0.9094
20	d C	AA	3	0.4696	0.4961	0.5060	0.5092	0.5108	0.5114	0.5119
21	d C	CE	4	0.4672	0.4924	0.5035	0.5073	0.5086	0.5101	0.5102
22	d W	AA	(1)	0.0043	0.0059	0.0071	0.0081	0.0088	0.0097	0.0099