Table 3

Site models and tests of selection
Model Parameter estimates ĸ lnL p
M0 ω = 0.070 1.01 −1961.39 <<0.001
M3 p0 = 0.585 p1 = 0.383, p2 = 0.032 0.98 −1922.15
ω0 = 0.001, ω1 = 0.151, ω2 = 0.615
M1 p0 = 0.952, p1 = 0.048, 1.13 −1946.80 --
ω0 = 0.057 ω1 = 1.000
M2 p0 = 0.952, p1 = 0.048, p2 = 0.000, 1.13 −1946.80
ω0 = 0.057, ω1 = 1.000, ω2 = 42.1
M7 p = 0.260, q = 2.948 0.94 −1924.53 --
M8 p0 = 1.000, p = 0.260 0.94 −1924.53
q = 2.95, (p1 = 0.000), ω = 2.51

Model refers to the Nsites value in codeml (e.g. M0 is nSites = 0); other parameter values for all tests were: codon frequency =3, model =0, omega = 0; ω is dN/dS and pn is the proportion of codons with ration ωn; κ is the transition:transversion ratio; LnL is the log likelihood, p is the result of χ2 test, which was not performed when the likelihoods were identical.

Gribble and Mark Welch

Gribble and Mark Welch BMC Evolutionary Biology 2012 12:134   doi:10.1186/1471-2148-12-134

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