Comparison of our statistical test performance for three choices of tree reconstruction methods: NJ (red/crosses), ML (blue/circles), and BI (red/X’s). Trees were reconstructed using PHYLIP, MrBayes and PhyML. A and B show comparisons of ROC curves on simulated data. See the section ROC Curves and False positive plots for a description of the ROC curve. C and D show comparison of curves on false positive rates (Y axis) vs. α levels (X axis). Panels A and C are for dissimilarity map-based tree space; panels B and D are for topological dissimilarity map. In C and D, the Y axis gives the p-values which are less than the α level (X axis).