Appendix 1—table 4. Predicted concordantly evolving pairs of sites for the simulated data with positively and negatively epistatically interacting sites.

The characteristics of predicted site pairs for the estimated FDR≤10% are shown: positions of sites on the primary sequence of S-protein (site1 and site2), the upper p-values (p-value), values of the epistatic statistic (epistat), numbers of consecutive pairs of mutations (#consec. pairs of mutations), numbers of mutations in consecutive pairs of sites (#mut. in consec. pairs in site1 and site2), total numbers of mutations on the internal tree branches in sites (#mut. in site1 and site2), the expected value of epistatic statistics (exp. epistat) and the corresponding standard error (SE). The true predictions are highlighted in bold.

site1	site2	p-value	epistat	#consec. pairs of mut.	#mut. in consec. pairs in site1	#mut. in consec. pairs in site2	#mut. in site1	#mut. in site2	exp. epistat	SE
1	2	<1e-4	12,36	66,5	52	65	2	96	3,97	0,87
3	4	<1e-4	17,79	94	61	104	4	118	6,55	1,23
5	6	<1e-4	13,87	54	48	54	6	105	3,27	0,83
5	43	<1e-4	21,43	108,5	82	100	43	105	12,6	1,89
7	8	<1e-4	11,36	50	42	50	8	109	3,22	0,78
9	10	<1e-4	17,09	90	64	88	10	117	6,62	1,19
11	12	<1e-4	13,46	53,5	48	51	12	108	2,54	0,69
13	14	<1e-4	11,63	52,5	43	56	14	106	2,85	0,72
15	16	<1e-4	11,84	69	47	70	16	116	5,88	1,08
19	20	<1e-4	9,06	47	39	47	18	109	4,29	0,88
48	68	<1e-4	29,11	171,5	110	169	20	95	2,6	0,69
17	18	2e-4	8,23	66	38	65	31	95	6,61	1,23
19	31	2e-4	11,58	78,5	56	78	67	176	20,72	2,09
50	94	2e-4	24,34	162,5	100	151	68	183	17,55	1,9
78	94	2e-4	28,50	172	110	169	94	178	20,5	2,07