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Table 2 atpB dataset: estimates for the first-order Markov chain distribution at the ancestral root sequence (for the GTR123+Γ123+CP123+F123+FF16+3F model).

From: Context-dependent codon partition models provide significant increases in model fit in atpB and rbcL protein-coding genes

 

Root

X

Ï€ X|A

Ï€ X|C

Ï€ X|G

Ï€ X|T

A

0.5049

[0.38; 0.61]

0.4089

[0.28; 0.52]

0.0382

[0.00; 0.13]

0.0480

[0.00; 0.16]

C

0.1018

[0.00; 0.31]

0.2481

[0.01; 0.75]

0.1993

[0.01; 0.55]

0.4507

[0.06; 0.79]

G

0.0402

[0.00; 0.15]

0.1610

[0.00; 0.52]

0.1088

[0.01; 0.40]

0.6899

[0.16; 0.94]

T

0.1010

[0.01; 0.25]

0.3925

[0.22; 0.54]

0.4490

[0.29; 0.59]

0.0575

[0.00; 0.20]

  1. Shown are mean estimates of 100.000 MCMC iterations, discarding the first 20.000 iterations as the burn-in, and the corresponding 95% credibility intervals. Despite the wide 95% credibility intervals, the estimates show why such a first-order dependence is useful.
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BMC Ecology and Evolution

ISSN: 2730-7182

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