R

Visualizing BEAST 2 time trees

The summary of the posterior from a Bayesian tip-dating analysis – e.g., the maximum clade credibility tree computed by TreeAnnotator from a BEAST 2 posterior – usually provides a whole wealth of information to the user, and while barebones, quick-and-dirty plotting of the results using FigTree or plot.phylo() is good enough for assessing whether the results are reasonable or not, it definitely doesn’t provide publication-quality figures. Below, I’ll try to show how such figures can be made by combining several existing R packages.