Fig. 4

Two visualizations of Quartet internode resolution (QIRP), polytomy (QIPP), and homoplasy (QIHP) probability calculations in PhyInformR using a focal node of bichirs (most recent common ancestor of Polypterus congicus and P. ansorgii) with Bayesian time trees and RAG1 sequence data from Near et al. [18]. a Violin plots displaying the kernel probability density of each of the three calculations across the posterior distribution of trees for the focal node with box plots of the quartiles for each distribution overlaid within. b–d Frequency plots for comparing QIRP (b), QIPP (c), and QIHP (d) against the length of internode. All points are sampled from the posterior. Color indicates the frequency of the joint QI measure and internode length within the posterior. In the Near et al. [18] tree from which this internode came, this internode was unresolved; this plot demonstrates that in most samples from the posterior, internode length was short, conferring little power to resolve branching order