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Table 9 Evaluation of the choice of codon equilibrium frequencies.

From: Comparative analysis of protein coding sequences from human, mouse and the domesticated pig

  

Estimated Branch Lengths

    

Model

df

Human

Mouse

Pig

κ

ω

lnL

X 2

FQ

1

0.136

0.340

0.178

2.862

0.125

-1502578

249354

F1 × 4

3

0.134

0.335

0.175

2.776

0.122

-1500436

231560

F3 × 4

9

0.136

0.343

0.178

2.692

0.119

-1495232

133363

F3 × 4 + CpG

10

0.138

0.351

0.181

2.593

0.114

-1493996

74214

Codon Table

60

0.136

0.348

0.179

2.497

0.113

-1478877

0

  1. The values are estimated with the concanated gene comprising 240,048 codons using the one ratio model. (df) Number of parameters (κ) Transition/transversion ratio. (ω) dN/dS ratio. (X2) A chi square test statistic comparing the expected frequencies of each codon to the observed codon counts.
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BMC Biology

ISSN: 1741-7007

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