Model Parameters for Phylogenetic Analysis
Viral gene		HIV-1-B enva		SIV envb
model class		GTR+I+G		GTR+I+G
fA		0.34857		0.3516
fC		0.17125		0.1642
fG		0.23694		0.2296
fT		0.24324		0.2546
RA<->C		1.971		1.8418
RA<->G		4.315		10.9127
RA<->T		0.8539		0.5803
RC<->G		1.021		0.9283
RC<->T		3.826		6.8499
RG<->T		1		1
p-inv		0.26035		0.471
gamma shape (α)		0.50434		0.9477

^a: Model parameters estimated using hierarchical likelihood ratio test with Modeltest, version 2.0, and PAUP* version 4.0b2.
^b: Model parameters estimated using Akaike Information Criterion (AIC) with Modeltest, version 3.06, and PAUP* version 4.0b10.


HIV-1 env sequences used for phylogenetic reconstruction

Sequence name	Accession number	Subtype
HIVELICG	K03454	D
HIVNDK	M27323	D
HIVZ2Z6	M22639	D
87USSG3X	L02317	B
88USWR27	U26546	B
89SP061	AJ006287	B
AUC18	AF042102	B
AUC18MBC	U37270	B
AUMBC200	AF042100	B
AUMBC925	AF042101	B
AUMBCC18B	AF042106	B
AUMBCC54	AF042103	B
AUMBCC98	AF042104	B
AUMBCD36	AF042105	B
USAD8	U19647	B
USDH123	AF069140	B
CNRL42CG	U71182	B
D31	U43096	B
HIVBH102	M15654	B
HIVCAM1	D10112	B
HIVF12CG	Z11530	B
HIVHAN2	U43141	B
HIVJC16	AF049494	B
HIVJRCSF	M38429	B
HIVJRFL	U63632	B
HIVLAICG	K02013	B
HIVMCK1	D86068	B
HIVMN	M17449	B
HIVNL43	M19921	B
HIVNY5CG	M38431	B
HIVOYI	M26727	B
HIVPV22	K02083	B
HIVRF	M17451	B
HIVSF2CG	K02007	B
HIVWEAU160	U21135	B
HIVYU10X	M93259	B
HIVYU2X	M93258	B
MANC	U23487	B
NLACH320A	U34603	B
NLACH320B	U34604	B
US89.6	U39362	B