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. 2021 Mar 15;7(3):mgen000511. doi: 10.1099/mgen.0.000511

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© 2021 The Authors

This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.

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Fig. 2. — Phylogenetic tree inferred from core SNPs with LESB58 GIs and prophages masked. Recombinant sites determined by ClonalFrameML were excluded. The GTR+F+G4 substitution model was selected by IQ-TREE and there were 2947 informative sites. The tree was visualized by iTol [47] with colour strip and branch colours indicating PHE designated regions of isolation or Canada. For visualization branch lengths >70 SNPs were truncated and marked with a star. Plotted around the tree is a heatmap of percentage identity with LESB58 prophage and GI regions, prophages 2–6 and GIs 1–5.