TABLE 3.
Likelihood ratio tests for positive selection of amino acid sites for HPV58 genes
| ORF | CODEML |
FUBAR |
|||||||
|---|---|---|---|---|---|---|---|---|---|
| Best modela | Log likelihood | dN/dS ratiob | LRT statisticc | Codond | dN/dS ratio | Posterior probabilitye | dN/dS ratio | Posterior probabilityf | |
| E6 | M3 | −779.5126 | 0.5853 | 21.4206 | 46V | 12.32 | 1.000 | 17.12 | 0.979 |
| 86D | 12.32 | 1.000 | 5.57 | 0.876 | |||||
| 93K | 12.32 | 1.000 | 9.25 | 0.947 | |||||
| 97N | 12.32 | 1.000 | 9.54 | 0.949 | |||||
| E7 | M2 | −606.8498 | 0.8527 | 16.3474 | 9R | 10.09 | 0.999 | 8.37 | 0.947 |
| 63G | 10.09 | 1.000 | 20.91 | 0.989 | |||||
| 64T | 8.47 | 0.833 | 9.45 | 0.919 | |||||
| 77V | 9.98 | 0.988 | 5.20 | 0.877 | |||||
| E1 | M3 | −3,452.3510 | 0.2046 | 1.8435 | |||||
| E2 | M8 | −1,986.1880 | 0.3243 | 23.1108 | 282V | 30.71 | 1.000 | 20.66 | 0.992 |
| E4 | M3 | −629.6729 | 1.9275 | 26.0371 | 1L | 15.92 | 1.000 | 8.72 | 0.913 |
| 39S | 20.47 | 1.000 | 7.73 | 0.908 | |||||
| 74V | 19.08 | 1.000 | 7.46 | 0.940 | |||||
| E5 | M2 | −442.6889 | 0.0744 | 0.0003 | |||||
| L2 | M3 | −2,918.3903 | 0.3219 | 0.0705 | |||||
| L1 | M3 | −3,182.2828 | 0.1830 | 17.7128 | 150L | 5.82 | 0.957 | 19.87 | 0.981 |
| 325I | 5.97 | 0.984 | 2.30 | 0.851 | |||||
| 375T | 6.06 | 1.000 | 8.46 | 0.955 | |||||
a
The “best” model was interpreted from the maximum log-likelihood value. M2, selection; M3, discrete; M8, beta and ω.
b
Overall dN/dS ratio for each gene.
c
Likelihood ratio test statistics follow a χ2 distribution, with degrees of freedom equaling 2 when values were ≥5.99 and P values were ≤0.05 (in boldface type).
d
Amino acid sites under positive selection are shown in boldface type.
e
Positively selected sites with P values of ≥0.950 by CODEML.
f
Positively selected sites with P values of ≥0.900 by FUBAR.