Graphs depicting the performance of the SVM-based test in detecting differences between gene trees reconstructed from simulated data using NJ. Trees were reconstructed using PHYLIP. Three different tree comparisons are used: one gene tree from species 1 versus 10 gene trees from species 2 (A and D), one gene tree from species 1 versus 50 gene trees from species 2 (B and E), and 10 gene trees from species 1 versus 10 gene trees from species 2 (C and F). In all graphs, we denote red lines with crosses topological dissimilarity maps and blue lines with circles standard dissimilarity maps of trees. A, B, and C show ROC curves on the simulated data from gene trees generated under different species trees. See the section ROC Curves and False positive plots for a description of the ROC curve. D, E, and F show curves for false positive rates vs. α-levels on the simulated data with gene trees generated under the same species trees. In D, E, and F, the X axis represents the α-levels and the Y axis represents the false positive rates.