Exchanging 10% of the sites: Maximum likelihood

The figure contains three graphs, which show the posterior probabilities for the three possible tree topologies, plotted along the DNA sequence alignment (the horizontal axis represents sites in the alignment).

Row	Posterior probability for
top	topology 1
middle	topology 2
right	topology 3

The location of the breakpoint (in the middle of the alignment at site 200) is fairly accurate, and the nature of the mosaic structure has been identified correctly in that a recombination event corresponding to a change from topology 1 (left) to topology 3 (right) is predicted. However, the predicted probability is wrong. The true probability for topology 3 in the right region is 0.9, while the predicted value is about 1.0.

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