Exchanging 10% of the sites: Bayesian MCMC

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, as opposed to maximum likelihood, the method also gives a reliable estimation of the uncertainty of the prediction. The predicted probability for topology 3 is about 0.9, that is, close to the true value.

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