Skip to main content

Table 4 rbcL 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

0.4225

[0.33; 0.51]

0.5464

[0.46; 0.64]

0.0159

[0.00; 0.06]

0.0151

[0.00; 0.06]

C

0.4454

[0.23; 0.69]

0.0111

[0.00; 0.04]

0.0364

[0.00; 0.11]

0.5071

[0.26; 0.73]

G

0.0164

[0.00; 0.07]

0.0147

[0.00; 0.06]

0.1294

[0.05; 0.25]

0.8395

[0.71; 0.93]

T

0.3319

[0.17; 0.48]

0.2020

[0.11; 0.31]

0.2660

[0.14; 0.43]

0.2001

[0.07; 0.34]

  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. Based on the mean estimates, many differences with the estimates of the atpB dataset, shown in Table 2, can be seen.