Evidence of Extensive Homologous Recombination in the Core Genome of Rickettsia

Figure 3

The phylogenetic compatibility matrix of Rickettsia’s core genes. The matrix is plotted based on the concatenated alignment of core genes with a 300-bp window and a 100-bp step. Phylogenetic trees are generated for each region using the neighbor-joining algorithm with a 70% bootstrap value. Phylogenetic violations of different topologies are calculated by comparison of the violations of the branching orders in different phylogenetic trees. Frequency is colored to indicate the number of phylogenetic violations per sequences.