Table 5.

Maximum likelihood (ML) estimates for 56 merged 3'-end ORFs of SARS-CoV

Models	d.f.	Parameters under null model	Parameters under alternative model	lnL0 (lnL1)	2Δl	P-value	Positively selected sites*
Branch Model M0 vs. FR	108	M0 (one ratio) ω = 0.170	Free Ratio ω = 0~∞	-9142.692 (-9055.881)	173.623	< 0.001	Not allowed
Site Model M0 vs. M3	4	M0 (one ratio) ω = 0.170	M3 (discrete, K = 3) p0= 0, ω0= 0 p1= 0.866, ω1= 0.058 (p2= 0.134),ω2= 0.986	-9142.692 (-9093.135)	99.114	< 0.001	None
Branch-site model A
BSL group as foreground MA' vs. MA	1	MA' (fix ω2= 1) p0= 0.868, ω0= 0.059 p1= 0.132 (p2a+p2b = 0)	MA p0= 0.868, ω0= 0.059 p1= 0.132, ω2= 1.000 (p2a+p2b = 0)	-9093.137 (-9093.137)	0	1.000	None
PC03 group as foreground MA' vs. MA	1	MA' (fix ω2= 1) p0= 0.868, ω0= 0.059 p1= 0.132 (p2a+p2b = 0)	MA p0= 0.868, ω0= 0.059 p1= 0.132, ω2 = 1.000 (p2a+p2b = 0)	-9093.137 (-9093.137)	0	1.000	None
HPEM group as foreground MA' vs. MA	1	MA' (fix ω2= 1) p0= 0.855, ω0= 0.059 p1= 0.130 (p2a+p2b = 0.015)	MA p0= 0.861, ω0= 0.059 p1= 0.131, ω 2= 4.300 (p2a+p2b = 0.008)	-9093.127 (-9093.088)	0.078	0.780
HPML group as foreground MA' vs. MA	1	MA' (fix ω2= 1) p0= 0.125, ω0= 0.047 p1= 0.017 (p2a+p2b = 0.858)	MA p0= 0.772, ω0= 0.046 p1= 0.106, ω 2= 9.863 (p2a+p2b = 0.122)	-9069.427 (-9065.120)	8.614	0.003	11, 29, 85, 129, 136, 222, 279, 280, 304, 319, 377, 388, 418, 423, 436, 449, 463, 469, 504, 584, 696, 850, 932, 954, 993
PCHP04 group as foreground MA' vs. MA	1	MA' (fix ω2= 1) p0= 0.690, ω0= 0.055 p1= 0.097 (p2a+p2b = 0.213)	MA p0= 0.862, ω0 = 0.057 p1= 0.119, ω 2= 22.447 (p2a+p2b = 0.019)	-9087.427 (-9076.176)	22.502	< 0.001	25, 259, 609, 1184
SARS group as foreground MA' vs. MA	1	MA' (fix ω2 = 1) p0 = 0.664, ω0= 0.033 p1= 0.066 (p2a+p2b = 0.270)	MA p0= 0.804, ω0= 0.037 p1= 0.074, ω 2= 3.138 (p2a+p2b = 0.122)	-9058.932 (-9051.231)	15.402	< 0.001	11, 15, 81,117, 120, 121, 171, 193, 259, 355, 361, 560, 609, 628, 830, 850, 1184

* Positively selected sites were identified with posterior probability p > 90%. In boldface, p > 95%.