Fig. 5.

Results from the 4-taxa data simulated using the BARGE program of Husmeier (2005). The solid line corresponds to topology 1, the dashed line to topology 2 and the dotted line to topology 3. We have successfully recovered the recombination events. The bottom plots show the posterior probability for the different states in the rate HMM. The values of the average branch length are restricted to {0.001, 0.003, 0.01, 0.03, 0.1, 0.3, 1.0, 3.0, 10.0, 100.0}. Only rates with a posterior P ≥ 0 are shown in the plot. The proposed method has picked up a change in rate between sites 800 and 900.