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Maximum-likelihood phylogenetic tree based on core-genome SNPs from 339 C. difficile isolates. Sequence data had been published previously (Dingle et al., 2013; He et al., 2013; Knetsch et al., 2014) and was retrieved from GenBank (https://www.ncbi.nlm.nih.gov/genbank/). Enlargements show details of collapsed branches. Blue squares indicate the presence of ABC transporter genes CDR20291_0805 and CDR20291_0806, and yellow squares indicate the lack of these two genes.
