Skip to main content

Table 7 Parameter values used in simulations of two-partition datasets.

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

 

Homogeneous parameter values

Heterogeneous parameter values

 

partition 1

partition 2

partition 1

partition 2

Rates

c1 = 1

c2 = 1

c1 = 1

c1 = 1

c2 = 3

c2 = 9

Selection pressure

ω1 = 0.25

ω1 = 0.75

ω1 = 2.25

ω2 = 0.25

ω2 = 0.75

ω2 = 2.25

ω1 = 0.25

ω1 = 0.75

ω1 = 0.25

ω2 = 0.75

ω2 = 2.25

ω2 = 2.25

Ts/Tv ratio

κ1 = 1.25

κ2 = 1.25

κ1 = 1.25

κ2 = 3.75

Codon frequencies

Ï€ i 1 = 1/61

Ï€ i 1 = lysin

Ï€ i 2 = 1/61

Ï€ i 2 = lysin

Ï€ i 1 = 1/61

Ï€ i 1 = lysin

Ï€ i 2 = lysin

Ï€ i 2 = 1/61

  1. The lysin gene was used to obtain empirical estimates of codon frequencies, this is indicated in the table by π i = lysin.