Fig. 5

Cladograms showing evolutionary relationship of E. coli O157 strain NADC 6564 to other pathogenic O157 and non-O157 strains. a Cladogram produced by constructing concatenated core genomes from whole genome sequences of 40 bacterial strains listed in Additional file 6: Table S1. A total of 2284 core genes were identified among the 40 strains used for constructing core genomes. These core genomes were used to infer a maximum likelihood phylogenetic tree using IQTREE. The generated tree was visualized using FigTree. Since there was no outgroup included in the tree, FigTree’s midpoint rooting method was used to root the tree. b Cladogram inferred using the parSNP-Gingr pipeline. Whole genomes for the sequences being compared were provided as input to parSNP using the NADC 6564 annotated GenBank file as the reference. Evolutionary trees were created by visualizing the parSNP output in Gingr