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

Table 2 An expanded set of fixed-effect models.

	Parameters heterogeneous among partitions
New code	κ	ω	c	π	Number of parameters
1 (E)	Yes	Yes	Yes	Yes	b+12g-1
2 (D)	Yes	Yes	Yes	No	b+3g+8
3	Yes	Yes	No	Yes	b+11g
4	Yes	Yes	No	No	b+2g+9
5	Yes	No	Yes	Yes	b+11g
6	Yes	No	Yes	No	b+2g+9
7	Yes	No	No	Yes	b+10g+1
8	Yes	No	No	No	b+g+10
9	No	Yes	Yes	Yes	b+11g
10	No	Yes	Yes	No	b+2g+9
11	No	Yes	No	Yes	b+10g+1
12	No	Yes	No	No	b+g+10
13 (C)	No	No	Yes	Yes	b+10g+1
14 (B)	No	No	Yes	No	b+g+10
15	No	No	No	Yes	b+9g+2
16 (A)	No	No	No	No	b+11

Number of parameters is for the F3 × 4 method of estimating codon frequencies. b and g denote the number of branches and the number of site classes, respectively. Letters in parentheses indicate the model codes formerly used by Yang and Swanson [4].

ISSN: 2730-7182