Table 7.
Results of maximum likelihood models of the Rhro-DRB sequences
| Model | k | l | Parameters estimates | Positively selected sites |
|---|---|---|---|---|
| M0 (one ratio) | 1 | − 1830.09 | ω = 0.559 | None |
| M1a (nearly neutral) | 1 | − 1690.63 | p0 = 0.603 (p1 = 0.397) | Not allowed |
| M2a (positive selection) | 3 | − 1653.33 |
p0 = 0.576, p1 = 0.400 (p2 = 0.025), ω2 = 12.820 |
11F, 13S |
| M3 (discrete) | 5 | − 1651.07 |
p0 = 0.602, p1 = 0.374 (p2 = 0.025), ω0 = 0.035, ω1 = 1.496, ω2 = 16.973 |
6R, 9E, 10Q, 11F, 13S, 15C, 25R, 26Y, 28Q, 30Y, 31F, 32Y, 37Y, 38 V, 47F, 49A, 56P, 57 V, 60 N, 61F, 63S, 64Q, 67F, 70Q, 71R, 72R, 74Q, 77 N, 78Y, 84G, 85 V, 86 V |
| M7 (beta) | 2 | − 1686.84 | p = 0.079, q = 0.125 | Not allowed |
| M8 (beta and omega) | 4 | −1651.44 | p0 = 0.975 (p1 = 0.025), p = 0.019, q = 0.035, ω = 11.880 | 11F, 13S |
K represents the number of parameters in the ω distribution, ω is the parameter of selection, pn is the proportion of sites falling into the ωn sites class. For models M7 and M8, p and q are the shape parameters of the β function. Sites inferred under selection at the 99% level are listed in bold, and those inferred at the 95% level are shown in italics