Fig. 3

Screen shots of Tree Analysis tab of VMCMC for an MCMC trace obtained from JPrIME on the tetrapod dataset “DS1” collected by Hedges et al. [25] The figure shows the “Tree Analysis” tab for the trace given in Additional file 3. The right panel visualizes pairwise distances between trees in the posterior distribution using a multi-dimensional scaling technique [19]. The panel can be used to assess mixing for the tree parameter and to visualize groups of trees that have been traversed during the run. Circle sizes reflect posterior probability and color has no significance other than to improve legibility. In this example, T1 seems to be distant from T0 and T2, and the chain appears to be sampling from these trees and trees around them without remaining on intermediate trees. This indicates, in agreement with Whidden et al. [27], that the DS1 dataset has a bimodal distribution. Presence of many trees in the vicinity of T0, T1, and T2, also indicates that the chain is mixing well for the tree parameter