TABLE 3.

Positively selected amino acid positions for HSV-1 and HSV-2 starting from the first codon in the reference sequence using five methods

Region	Product	Amino acid position(s)
		FEL (0.1)a	SLAC (0.1)b	iFEL (0.1)a	MEME (0.1)a	FUBAR (0.9)c	Agreementd
UL	gL-1	212		212	212	157, 171, 212	212
	gL-2					37
	gM-1	203	203	203	203	203	203
	gM-2			13, 243
	gH-1	284	284	284	284, 369	284, 369, 370	284
	gH-2	516, 634	516	516	634	112, 154, 516, 634	516, 634
	gB-1	59			549
	gB-2	7, 336, 851	336, 402, 851	7, 336, 851	7, 43, 336, 488, 851	7, 42, 55, 336, 402, 851	7, 336, 851
	gC-1	23, 289, 306, 366	23, 289, 306, 366	23, 75, 132,242, 262, 289, 309, 349	16, 23, 71, 80, 132, 242, 245, 248, 262, 264, 289, 305, 306, 383, 393, 414, 424	16, 23, 132, 262, 289, 300, 306, 366, 424	23, 289, 306, 366
	gC-2	53	344, 428	194	53, 194, 195	53, 169, 214	53
	gN-1
	gN-2
	gK-1	224		224, 309	40, 224, 226, 309, 325	224	224
	gK-2				247	115, 247
US	gG-1	3, 167, 225, 238	167	97, 166, 167, 207	3, 167, 207, 214, 238	3, 97, 167, 238	3, 167, 238
	gG-2	204, 212, 291, 338, 426	204, 338, 426	204, 212, 291, 338, 400, 426, 569	136, 204, 212, 291, 331, 338, 400, 426, 469, 562, 563, 604	35, 136, 204, 212, 291, 328, 338, 349, 408, 426, 445, 512, 592	204, 212, 291, 338, 426
	gJ-1		60	25		54, 60, 91
	gJ-2					30, 86
	gD-1			50	84, 369, 374
	gD-2			353
	gI-1			189, 297	18, 179, 189, 297	18, 179, 189, 221, 222	189
	gI-2	246		215, 246		120, 259
	gE-1		188	259		120, 259
	gE-2			194		43, 51, 410

^aThe number in parentheses is the cutoff P value for the single degree of freedom likelihood ratio test to classify a site as positively selected.

^bThe number in parentheses is the cutoff P value for the two-tailed extended binomial test to classify a site as positively selected.

^cThe number in parentheses is a cutoff value for the Bayes factor for the event of positive selection at a given site, sel 2.

^dAt least three methods indicated positive selection at the coding position(s) listed; boldface indicates agreement among all selection methods.