Accurate Detection of Recombinant Breakpoints in Whole-Genome Alignments
Figure 6
We confirm Filho et al.'s breakpoints near 1322 and 2571 (red), and predict new recombinant regions in nt 4784–4945 as well as 970–1049 (green). The second of these is short, but present in some form in all three strains analyzed here. The spike at 3851–3909 is even shorter and is not represented in the other two species, leading us to not predict it as a likely recombinant region. Trees trained in hidden states are shown below the plot.