Table 4. Positive and negative selection results for West Nile virus isolates, Upper Texas Gulf Coast, USA, 2002–2009*.

Protein	Amino acid residues relative to ORF	Length of protein, aa	Overall dN/dS	Single-likelihood ancestor counting†			Fixed effects likelihood†			Internal fixed effects likelihood†
				Positive selection	Negative selection		Positive selection	Negative selection		Positive selection	Negative selection
ORF	1–3,333‡	3,333	0.110	2	246		8	619		16	25
C	1–123	123	0.270	0	2		0	9		0	2
prM	124–290	166	0.134	0	7		0	25		1	3
E	291–791	500	0.119	0	15		1	72		1	3
NS1	792–1143	351	0.134	0	17		1	48		4	4
NS2A	1144–1374	230	0.130	0	15		1	48		1	3
NS2B	1375–1505	130	0.118	0	6		0	19		0	1
NS3	1506–2124	618	0.083	0	42		0	101		0	6
NS4A	2125–2273	148	0.135	0	7		1	22		0	3
NS4B	2274–2522	248	0.112	0	13		0	49		0	8
NS5	2529–3433	904	0.098	0	61		2	148		4	10

*ORF, open reading frame; d_N, nonsynonymous nucleotide substitutions; d_S, synonymous nucleotide substitutions; C, capsid; prM, premembrane; E, envelope; NS, nonstructural.
†No. sites where p<0.1.
‡Only the first 3,333 aa residues of the ORF were used for these analyses because of program constraints on alignment size.