Table A1.

Short-sequences data set. Average RF distance for each reference set of the synthetic short-sequences data set (sequence length of 300 amino acids, no ASRV). Order of methods and values for k are determined as in Table 1. The Friedman test statistic is F_R = 3693.4 (P < 10⁻¹⁰). Significant differences are found at or beyond the α = 0.05 level between the following pairs (numbers refer to column “No.”): method 1 versus methods 22–2, methods 2 and 3 versus methods 22–4; methods 4 and 5 versus methods 22–6; methods 6–19 versus methods 22–20; and methods 20 and 21 versus method 22.

					Reference set of short-sequences data
No.		Method		k	1	2	3	4	5	6	7
1	3624.5	d ML	AA	—	0.060	0.102	0.138	0.178	0.244	0.304	0.350
2	4765.5	d PB-ML	CE	—	0.076	0.108	0.172	0.218	0.360	0.492	0.632
3	4836.5	d PB-SIM	CE	—	0.064	0.098	0.176	0.218	0.356	0.534	0.658
4	5827.5	d PB-ML	AA	—	0.080	0.106	0.198	0.266	0.498	0.662	0.750
5	5984.0	d PB-SIM	AA	—	0.062	0.100	0.204	0.272	0.504	0.712	0.764
6	8171.5	d P	CE	5	0.110	0.180	0.308	0.456	0.684	0.794	0.838
7	8206.5	d ACS	CE	—	0.112	0.180	0.312	0.464	0.670	0.806	0.830
8	8251.0	d E	CE	5	0.096	0.170	0.338	0.462	0.700	0.798	0.850
9	8258.5	d P	AA	4	0.074	0.146	0.322	0.468	0.714	0.802	0.892
10	8359.0	d F	CE	5	0.108	0.186	0.328	0.468	0.706	0.792	0.842
11	8442.0	d E	AA	4	0.068	0.156	0.322	0.490	0.730	0.816	0.890
12	8456.5	B-bin	CE	4	0.106	0.170	0.370	0.486	0.706	0.784	0.834
13	8475.5	d F	AA	4	0.078	0.146	0.330	0.492	0.728	0.820	0.892
14	8479.5	d ACS	AA	—	0.088	0.158	0.338	0.526	0.702	0.802	0.854
15	8558.5	d LZ	CE	—	0.092	0.162	0.332	0.514	0.744	0.822	0.838
16	8628.5	d S	CE	5	0.128	0.222	0.362	0.492	0.696	0.794	0.808
17	8697.0	d LZ	AA	—	0.068	0.154	0.334	0.544	0.762	0.842	0.860
18	8791.5	B-bin	AA	3	0.086	0.176	0.354	0.538	0.738	0.852	0.832
19	9016.5	d S	AA	4	0.104	0.244	0.358	0.524	0.730	0.816	0.868
20	10,198.0	d C	AA	3	0.116	0.252	0.444	0.614	0.816	0.890	0.906
21	10,964.0	d C	CE	4	0.176	0.338	0.506	0.692	0.836	0.890	0.884
22	12,108.0	d W	AA	(1)	0.482	0.546	0.668	0.734	0.800	0.872	0.886