Skip to main content

Table 4 rbcL dataset: estimates for the first-order Markov chain distribution at the ancestral root sequence (for the GTR123123+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 π X|A π X|C π X|G π 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.