TABLE 6

Log-likelihood values under models M7, M8 (Yang et al. 2000), and M8a (Swanson et al. 2003) and parameter estimates under model M8 by PAML in the coding region

Log-likelihood values of the models
Data setM7M8M8aEstimates of parameters p, q, and ω in M8
Classical swine fever virus−365.60−365.47−365.60p0 = 0.53, p = 0.00, q = 1.52,
   (p1 = 0.47), ω = 0.59
Dengue virus type 1−23921.15−23919.40−23919.87p0 = 0.96, p = 3.06, q = 99.00,
   (p1 = 0.04), ω = 0.69
Ebola glycoprotein−8192.94−8188.12−8189.07p0 = 0.89, p = 0.49, q = 7.58,
   (p1 = 0.11), ω = 5.92
Foot-and-mouth disease−19071.89−19066.11−19066.11p0 = 0.97, p = 0.13, q = 2.34,
   (p1 = 0.03), ω = 1.01
Hepatitis A−11747.53−11746.19−11746.20p0 = 0.99, p = 1.78, q = 99.00,
   (p1 = 0.01), ω = 1.19
Hepatitis C−59726.45−59717.34−59720.92p0 = 0.99, p = 0.27, q = 2.36,
   (p1 = 0.01), ω = 73.73
Japanese encephalitis virus−28710.23−28708.87−28708.88p0 = 0.56, p = 0.09, q = 0.92,
   (p1 = 0.44), ω = 0.06
Mammalian orthoreovirus−13060.29−13058.67−13058.85p0 = 0.64, p = 0.02, q = 0.42,
   (p1 = 0.36), ω = 0.01
Newcastle disease virus−4787.83−4776.37−4785.65p0 = 1.00, p = 0.23, q = 1.59,
   (p1 = 0.00), ω = 99.00
Poliovirus−19803.71−19799.22−19799.50p0 = 0.96, p = 0.30, q = 2.83,
   (p1 = 0.04)
Rabies virus glycoprotein−11499.48−11497.40−11497.70p0 = 0.98, p = 0.33, q = 3.88,
   (p1 = 0.02), ω = 0.69
TT virus ORF 2−3666.58−3666.29−3666.35p0 = 0.84, p = 0.80, q = 0.99,
   (p1 = 0.16), ω = 1.13
West Nile virus−22769.51−22769.33−22769.51p0 = 0.95, p = 0.62, q = 99.00,
   (p1 = 0.05), ω = 0.14