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| Site class | Proportion | Background ω | Foreground ω |
| 0 | p 0 | 0<ω0<1 | 0<ω 0<1 |
| 1 | p 1 | ω1 = 1 | ω1 = 1 |
| 2a | (1−p 0−p 1)p 0/(p 0+p 1) | 0<ω0<1 | ω2≥1 |
| 2b | (1−p 0−p 1)p 1/(p 0+p 1) | ω1 = 1 | ω2≥1 |
Note. This is the alternative model of the branch-site test of positive selection.
The null model fixes ω2 = 1.
