Visualization of the comparison of the phylogenetic concordance.

To visualize the concordance of the four applied tree building methods, heatmaps were created which were calculated based on the particular absolute patristic distances for each isolate obtained by two different approaches A) the SNP-based (read-alignment and variant calling) approach and B) cgMLST analysis (based on de novo assembly), C) maximum common genome (based on de novo assembly) or D) feature frequency profiling (FFP; based on de novo assembly)—based phylogenetic trees. The left side of the heatmap depicts the phylogenetic tree which was used as reference for the comparison (A/B/C). On the top of the map are the phylogenetic trees for B) cgMLST, C) maximum common genome and D) FFP-based analyses. The heatmap color-codes the absolute difference of patristic distances of isolate pairs obtained by the respective phylogenetic analyses. Small differences in distances are shown in blue. Large differences in distances are shown in orange. The median of all values was calculated to lower the effect of logarithmic data distribution on the visualization and used as the mean value of the color scale, which is shown in gray (“13”). (PDF)