Table 3.

Codon (amino acid) sites found to be under episodic diversifying selection.

Codon	α	β−	Pr[β = β−]	β+	Pr[β = β+]	P-value	q-value
3	0.71267	0	0.87743	33.051	0.12257	0.0357189	0.446487
26	0.594053	0.219727	0.83171	8.61427	0.16829	0.0427582	0.493364
48	0.592732	0.0233223	0.499489	7.0793	0.500511	0.0111048	0.23796
58	0.626032	0.153589	0.886189	208.891	0.113811	0.0471447	0.441982
64	0.578003	0	0.743857	3.43805	0.256143	0.0465647	0.465647
71	0.134445	0	0.846411	32.9029	0.153589	9.0959e-05	0.0136439
76	0.706383	0.043358	0.572077	7.49808	0.427923	0.0137215	0.257279
80	1.14485	0	0.823905	8.58932	0.176095	0.044903	0.481103
84	5e-09	5e-09	0.694404	8.03456	0.305596	0.000501674	0.0376255
95	5e-09	2. 5e-17	0.589632	3.53825	0.410368	0.0140873	0.234789
99	0.608495	0	0.854247	10.7894	0.145753	0.00485977	0.242988
107	0.320033	0.320033	0.938072	40.1285	0.061928	0.0289885	0.434828
110	0.330462	0.282797	0.966787	190.886	0.033213	0.0102668	0.25667
116	5e-09	2. 5e-17	0.725722	7.7696	0.274278	0.00678347	0.25438
126	0.934956	0.871756	0.913601	222.694	0.086399	0.0303443	0.413787
130	0.637836	0.00500758	0.600822	6.96584	0.399178	0.0100967	0.3029

Notes: Codon = codon (or amino acid) number in the alignment; alpha = the maximum likelihood estimate (MLE) of the synonymoys substitution rate alpha; β⁻ = the maximum likelihood estimate (MLE) of the non-synonymous rate for the branch class with β smaller or equal to alpha; Pr[ β = β⁻] = the MLE of the proportion of sites evolving at β⁻ ; β⁺ = the MLE of the unconstrained β non-synonymous rate; Pr[ β = β⁺ ] = the MLE of the proportion of sites evolving at β⁺ ; P-value = the probability value for the likelihood ratio test statistic for β⁺ = alpha (null) versus β⁺ unrestricted (alternative); q-value = false discovery rate under the strict neutral null.