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Table 5 Maximum likelihood (ML) estimates for 56 merged 3'-end ORFs of SARS-CoV

From: Differential stepwise evolution of SARS coronavirus functional proteins in different host species

Models d.f. Parameters
under
null
model
Parameters
under
alternative
model
lnL0
(lnL1)
l 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
  1. * Positively selected sites were identified with posterior probability p > 90%. In boldface, p > 95%.