Figure 2.

Results of the ClonalFrame analysis on an alignment of the 12 C. trachomatis genomes. The inferred clonal genealogy is shown on the left. To each branch of this tree corresponds a row of the heat map, which is vertically aligned with it. Each row of the heat map shows the posterior probability of recombination estimated by ClonalFrame on the corresponding branch (Y-axis) and along the positions of the alignment (X-axis). These probabilities are color-coded according to the legend shown at the top.