Figure 3

PP -plots for lumpability tests for simulated data. PP-plots for the likelihood-ratio test, with respect to RY recoding, for the randomly-generated lumpable 7-taxon data (a) and the randomly-generated non-lumpable 7-taxon data (b). Sequences comprising 2000 sites were generated on the tree shown in Figure 4 under time-reversible conditions with sites evolving under independent and identical conditions ((a): π^T = (0.1, 0.2, 0.3, 0.4), and s^T = (0.20, 0.25, 0.20, 0.20, 0.15, 0.20); (b): π^T = (0.1, 0.2, 0.3, 0.4), and s^T = (0.50, 0.25, 0.20, 0.20, 0.15, 0.20)).