TABLE 2

Analysis of β-globin and HIV-1 pol for positively selected sites

Data setModel/testOptimal
 log-likelihoodOptimal parametersPositively selected sites
β-Globin M8A−3594.55κ = 1.78, p0 = 0.90,NA
p = 0.63, q = 3.24
 M8B−3591.83κ = 1.86, p0 = 0.94,7, 50, 67, 85, 123
p = 0.58, q = 2.44,
ω = 1.62
 SLRNAκ = 1.78, ω = 0.24None
HIV-1 pol M8A−9293.65κ = 4.87, p0 = 0.87,
 p = 0.70, q = 10.92NA
 M8B−9263.52κ = 5.29, p0 = 0.97,2, 3, 14, 41, 67, 347, 379, 459, 478, 568, 654, 761, 779
p = 0.19, q = 1.08,
ω = 3.78
 SLRNAκ = 4.84, ω = 0.202, 3, 4, 14, 41, 67, 313, 347, 379, 388, 431, 459, 462,
   478, 568, 570, 654, 732, 761, 779, 782, 890
  • Results of analysis of β-globin and HIV-1 pol data sets are shown, using the SNY test (models M8A and M8B) and the SLR test. For the SLR test, the parameter values given are those optimal under M0. The sites listed are those at which positive selection is detected with a cutoff (significance level or posterior probability, as appropriate to the method used) >95%; those >99% are in italics. The italic underlined sites are those at which there is still evidence for positive selection after correcting the SLR test for multiple comparisons.