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Rooted maximum credibility tree constructed from 1000 single copy orthologous proteins using BEAST.
We generated a Bayesian maximum credibility tree with mean node age inferred using BEAST, based on 1000 randomly selected single copy orthologs.
A maximum credibility tree was subsequently produced using TreeAnnotator v1.6.1.
A maximum credibility tree was generated from the combined trees in TreeAnnotater [ 83].
A maximum credibility tree was then produced using TreeAnnotator v1.5.3 [ 21].
The postburn-in information from convergent runs was combined to further estimate posterior distribution of topologies, as well as the maximum credibility tree.
Trees were combined into maximum credibility trees using TreeAnnotator version 1.8.1.
Runs were combined using LogCombiner, and maximum credibility trees with divergence time means and 95% highest probability densities (HPDs) were produced using Tree Annotator (both part of the BEAST package).
Tracer V1.5 [ 119] was used to evaluate the MCMC runs, TreeAnnotator v1.6.1 [ 95] and Figtree v1.3.1 were used to annotate and visualize maximum credibility trees listing all posterior probabilities.
Results from the four independent runs were then combined using LogCombiner, and maximum credibility trees with divergence time means and 95% highest probability densities (HPDs) were produced using TreeAnnotator v1.7.5 [ 121].
The sampled posterior trees were summarized using TreeAnnotator v.2 to generate a maximum clade credibility tree (maximum posterior probabilities) and calculate the median ages and 95%% highest posterior density (HPD) intervals for each node.
