Table 1.
Codeml analyses using site-specific models.
| TRIM5α | |||||
| Site-specific Modelsa | ω0b | ω1c | ω2d | LogL | Sites with ω > 1 e |
| C: M1a | 0.00 (34.91%) | 1.00 (65.09%) | -4117.12 | ||
| D: M2a | 0.00 (26.04%) | 1.00 (61.67%) | 6.37* (12.29%) | -4087.97 | 11 sites |
| APOBEC3G | |||||
| Site-specific Models | ω0 | ω1 | ω2 | LogL | Sites with ω > 1 |
| C: M1a | 0.03 (37.56%) | 1.00 (62.44%) | -4187.55 | ||
| D: M2a | 0.00 (28.28%) | 1.00 (48.60%) | 4.40* (23.11%) | -4148.85 | 24 sites |
| TRIM19 (PML) | |||||
| Site-specific Models | ω0 | ω1 | ω2 | LogL | Sites with ω > 1 |
| C: M1a | 0.09 (91.47%) | 1.00 (8.53%) | -5215.40 | ||
| D: M2a | 0.11 (97.25%) | 1.00 (0.00%) | 2.5 (2.75%) | -5214.46 | n/a f |
| PPIA (Cyclophilin A) | |||||
| Site-specific Models | ω0 | ω1 | ω2 | LogL | Sites with ω > 1 |
| C: M1a | 0.05 (100%) | 1.00 (0%) | -751.04 | ||
| D: M2a | 0.05 (100%) | 1.00 (0.00%) | 1.00 (0.00%) | -751.04 | n/a f |
a the likelihood models used are described in the text
b class of sites under purifying selection
c class of sites evolving neutrally
d class of sites that may show KA/KS > 1
e sites pinpointed to be under positive selection by Bayes Empirical Bayes analysis
f test not applicable (M1a and M2a not significantly different)