Highway plot and phylogenies for the CRF03_AB data set. In this plot, the horizontal axis represents the alignment sites, whereas the vertical axis indicates changes of topology and branch length of the inferred quartet trees along the alignment . The three 'lanes', which lie between the three horizontal lines in the plot, reflect the fact that a quartet tree can have three possible topologies. Each curve or 'trajectory' in the plot represents changes in the inferred quartet tree along the alignment for a particular quartet of sequences. Only the trajectories for the 50 top-ranking quartets are shown. Maximum likelihood trees for the three separate gene regions, separated by the breakpoints inferred from the quartet trajectory changes, are shown below the highway plot. The recombinant strains are indicated with a rectangle.