Table 2. Codons of DENV-2 under episodic diversifying selection identified using MEME method.

The codons under significant evidence of episodic positive selection (p < 0.05) were obtained in all the genes except for NS4A. The table provides MEME results such as distribution of synonymous (α) and non-synonymous (β) substitution rates over sites. The maximum likelihood estimate (MLE) of the non-synonymous rate for the branch class with β ≤ α is represented as ‘β −’. ‘Pr[β = β −]’ represents the MLE of the proportion of sites evolving at ‘β −’. The MLE of the unconstrained β non-synonymous rate is given as ‘β +’. The MLE of the proportion of sites evolving at β + is represented as ‘Pr[β = β +]’. The false discovery rate is controlled by the ‘q-value’, under the strict neutral null.

Sr. no.	Gene	Codon	α	β −	Pr[β = β −]	β+	Pr[β = β +]	p-value	q-value
1	C	11	0.164376	0	0.953173	21.9755	0.046827	0.005121	0.583832
2	M	147	0.159745	0	0.997987	3769.49	0.002013	5.37E−05	0.008919
3	E	91	1.7408	0.032332	0.992346	706.968	0.007654	0.009902	1
4	E	128	0	0	0.994362	305.675	0.005638	0.013207	1
5	E	192	1.61287	0	0.994973	544.37	0.005027	0.001674	0.828819
6	E	271	0.62851	0	0.998508	3578.71	0.001492	0.01428	1
7	E	340	0	0	0.998292	238.733	0.001708	0.004202	1
8	E	363	1.39999	0	0.99606	156.326	0.00394	0.00753	1
9	E	402	0.557236	0	0.996846	1009.79	0.003154	0.0285	1
10	E	455	0	0	0.996943	910.053	0.003057	0.021326	1
11	NS1	47	0.849852	0	0.996678	1630.99	0.003322	0.013512	1
12	NS1	146	0.182516	0	0.987198	92.3804	0.012802	0.015277	1
13	NS1	164	0.74287	0	0.981603	391.58	0.018397	0.000484	0.085203
14	NS1	181	0.498353	0	0.993067	176.231	0.006933	0.049911	1
15	NS1	207	0	0	0.995688	174.175	0.004312	0.000447	0.157292
16	NS1	230	1.78007	0	0.997897	182.989	0.002103	0.007617	0.893734
17	NS2A	16	0.409451	0	0.997886	2812.78	0.002114	5.39E−07	0.000118
18	NS2A	72	0.290106	0	0.993819	67.2445	0.006181	0.009687	0.351954
19	NS2A	111	0.477414	0	0.995018	32.6139	0.004982	0.019069	0.593865
20	NS2A	114	1.77037	0	0.996181	570.44	0.003819	0.005226	0.227852
21	NS2A	119	1.29922	0	0.99421	1136.87	0.00579	0.004792	0.261146
22	NS2A	140	0	0	0.998138	1625.9	0.001862	0.044979	1
23	NS2A	181	1.79665	0.205045	0.987651	757.326	0.012349	0.000884	0.09635
24	NS2A	199	0.884091	0	0.997546	168.309	0.002454	0.004221	0.306752
25	NS2B	63	1.48592	0.12202	0.992686	320.784	0.007314	0.001293	0.168124
26	NS3	14	0	0	0.86109	10.8058	0.13891	0.000166	0.102849
27	NS3	49	0	0	0.99844	216.962	0.00156	0.000191	0.059005
28	NS3	138	0.155937	0	0.998495	866.279	0.001505	0.004107	0.846078
29	NS4B	122	1.01576	0	0.995707	318.631	0.004293	0.000418	0.051883
30	NS4B	156	0.103265	0.103265	0.996932	3312.6	0.003068	0.000167	0.041538
31	NS5	5	0.546428	0.3356	0.986448	37.3205	0.013552	0.045428	1
32	NS5	6	0.151621	0	0.998617	1120.9	0.001383	0.00018	0.054024
33	NS5	25	0.934525	0	0.998355	329.819	0.001645	0.004794	0.862932
34	NS5	130	1.84523	0	0.99369	134.257	0.00631	0.031375	1
35	NS5	209	0.434112	0	0.998651	3523.06	0.001349	3.28E−07	0.000148
36	NS5	271	0	0	1.00E−09	1.65517	1	0.014739	1
37	NS5	400	0.508322	0	0.959072	11.2506	0.040928	0.022174	1
38	NS5	414	0.639643	0	0.996067	3523.04	0.003933	0.003799	0.854778
39	NS5	558	0	0	0.823609	3.9341	0.176391	0.010112	1
40	NS5	679	0	0	0.917709	2.65504	0.082291	0.023981	1
41	NS5	803	0	0	0.997137	1066.86	0.002863	1.75E−07	0.000158