Table A4.

Distances for ASRV data set. Median of calculated distances for each reference set of the synthetic ASRV data set (sequence length of 1000 amino acids, high ASRV with α = 0.5). Order of methods and values for k are as in Table 2.

				Reference set of ASRV data
No.	Method		k	1	2	3	4	5	6	7
1	d ML	AA	—	0.4635	0.6077	0.7746	0.9114	1.0031	1.1273	1.2114
2	d PB-ML	AA	—	0.7188	0.8724	1.0516	1.1905	1.2653	1.3803	1.4582
3	d PB-SIM	AA	—	5.1888	5.8917	6.5781	7.0346	7.2585	7.5753	7.7762
4	d PB-ML	CE	—	1.6066	1.8151	2.0460	2.2236	2.3105	2.4451	2.5255
5	d PB-SIM	CE	—	7.9433	8.3644	8.7589	9.0329	9.1515	9.3314	9.4407
6	d P	AA	4	0.6591	0.7971	0.8737	0.9111	0.9278	0.9431	0.9511
7	d E	AA	4	1612	1744	1834	1882	1904	1924	1938
8	d F	AA	4	1.2087	1.4550	1.6646	1.7946	1.8633	1.9301	1.9724
9	d LZ	AA	—	0.8026	0.8423	0.8678	0.8799	0.8854	0.8910	0.8942
10	d ACS	AA	—	1.0164	1.1450	1.2363	1.2858	1.3101	1.3347	1.3484
12	d P	CE	5	0.3952	0.5859	0.7109	0.7782	0.8081	0.8368	0.8528
13	d S	AA	4	0.2535	0.2764	0.2913	0.2995	0.3034	0.3081	0.3119
14	d LZ	CE	—	0.7958	0.8382	0.8631	0.8762	0.8821	0.8876	0.8902
15	d F	CE	5	1.0672	1.3031	1.4939	1.6150	1.6748	1.7413	1.7762
16	d E	CE	5	1556	1708	1808	1862	1888	1914	1926
17	d ACS	CE	—	0.7131	0.8085	0.8713	0.9053	0.9202	0.9359	0.9454
19	d S	CE	5	4.9359	5.4552	5.7908	5.9795	6.0650	6.1590	6.2287
20	d C	AA	3	0.4121	0.4457	0.4665	0.4783	0.4850	0.4906	0.4933
21	d C	CE	4	0.4167	0.4493	0.4711	0.4818	0.4877	0.4938	0.4972
22	d W	AA	(1)	0.0032	0.0040	0.0049	0.0053	0.0058	0.0062	0.0064