TABLE 1

Parameter estimates and log likelihood values under different models for the HIV-1 envelope gene

ModelYear 3Year 4Year 5Year 6Year 7
Goldman and Yangω6.2490.6400.7780.8030.358
κ2.5394.6285.5562.7964.163
l−537.22−457.07−483.66−588.89−555.54
Gamma-ratesω8.5240.8020.9900.9630.358
κ2.6624.5005.9302.7304.131
α0.2100.2470.1910.3440.588
l−520.14−448.61−471.71−574.28− 548.17
Neutralp10.4130.3340.3350.3920.379
p20.5870.6660.6650.6080.621
κ2.3054.5625.7252.7524.389
l−53i.94−450.66−474.93−576.23−546.09
Positive-selectionp10.7660.3940.1980.3690.359
p20.0180.5600.6450.5470.598
p30.2160.0460.1570.0840.043
ω329.53714.8936.9206.8497.709
κ2.6445.1476.0952.9005.051
l−519.06−444.68−470.32−570.15−543.67
Continuous neutralp10.4130.3340.3350.3920.379
p20.5870.6660.6650.6080.621
κ2.3054.5625.7252.7524.389
α
l−531.94−450.66−474.93−576.23−546.09
Continuous positive-selectionp10.7660.4570.4870.3690.406
p20.0180.4950.3410.5470.545
p30.2160.0470.1720.0840.049
ω329.53713.6516.4696.8496.504
κ2.6445.1606.1462.9005.062
α10.3150.5135.528
l−519.06−444.65−470.32− 570.15−543.42