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).

Root


X

πX|A

πX|C

πX|G

πX|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]


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.

Baele et al. BMC Evolutionary Biology 2011 11:145   doi:10.1186/1471-2148-11-145

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