Methods for selecting fixed-effect models for heterogeneous codon evolution, with comments on their application to gene and genome data

Table 6 Likelihood scores and parameter estimates obtained under the model selected by backward elimination for subsets of the genes located in the regions of the Listeria genome encoding putative flagellar related proteins.

			Parameter estimates
Dataset & numbered partitions	Model	ℓ	c	ω	κ
Rapidly-evolving non-flagellar genes [4 genes]	FE9	-8528.24
1. Chemotaxis regulatory protein			(c₁ = 1)	ω₁ = 0.0001	κ₁ = 1.77
2. Chemotaxis-related sensory protein			c₂ = 1.22	ω₂ = 0.03	κ₂ = κ₁
3. Cell surface protein			c₃ = 5.35	ω₃ = 0.17	κ₃ = κ₁
4. Phage-related, similar to transglycosylase			c₄ = 3.77	ω₄ = 0.05	κ₄ = κ₁
Flagellar related genes [24 genes]	FE13	-42796.43
1. flaA gene			(c₁ = 1)	ω₁ = 0.017	κ₁ = 1.96
2. 23 other genes			c₂ = 0.14	ω₂ = ω₁	κ₂ = κ₁

Number within square brackets is the number of genes in the dataset. Parentheses indicate a model parameter with a fixed value.

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