TABLE 2

Models of variable ω ratios among sites

Model codepParametersNotes
M0 (one-ratio)1ωOne ω ratio for all sites
M1 (neutral)1p0p1 = 1 − p0, ω0 = 0, ω1 = 1
M2 (selection)3p0, p1, ω2p2 = 1 - p0 - Pl, ω0 = 0, ω1 = 1
M3 (discrete)2K − 1p0, pl, … , pK-2,pK–1 = 1 – p0pl – … – pK–2
(K = 3)ω0, ω1, . . ωK–1
M4 (freqs)K–1 (K = 5)p0, pl, … , pK–2The ωk are fixed at 0, ⅓>, ⅔, 1, and 3
M5 (gamma)2α, βFrom G(α, β)
M6 (2gamma)4p0, α0, β0, α1p0 from G(α0, β0) and p1 = 1 – p0 from G(α1, α1)
M7 (beta)2p, qFrom B(p, q)
M8 (beta&ω)4p0, p, q, ωp0 from B(p, q) and 1 – p0 with ω
M9 (beta&gamma)5p0, p, q, α, βp0 from B(p, q) and 1 – p0 from G(α, β)
M10 (beta&gamma + 1)5p0, p, q, α, βp0 from B(p, q) and 1 – p0 from 1 + G(α, β)
M11 (beta&normal>1)5p0, p, q, μ σp0 from B(p, q) and 1 – p0 from N(μ σ2), truncated to ω > 1
M12 (0&2normal>1)5p0, pl, μ2, σl, σ2p0 with ω0 = 0 and 1 – p0 from the mixture: p1 from N(1, σ12), and 1 – p1 from N(μ, σ22), both normals truncated to ω > 1
M13 (3normal>0)6p0, pl, μ2, σ0, σl, σ2p0 from N(0, σ02), p1 from N(1, σ12), and P2 = 1 – p0 - Pl from N(μ2, σ22), all normals truncated to ω > 1
  • p, number of parameters in the ω distribution.