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. 2012 Apr 6;7(4):e33971. doi: 10.1371/journal.pone.0033971

Figure 3. E. coli O104:H4 phylogenies constructed based on the 3794 shared genes using different methodologies.

Figure 3

A), maximum likelihood tree of the concatenated sequences (3613248 characters). All branches are 100% bootstrap supported. The branch length separating IAI1 from the E. coli O104:H4 strains is not to scale and the length is shown. B), feature frequency profiles (FFPs) tree. ON2010 is shown to be distinct from the remaining E. coli O104:H4 strains and IAI1. The branch length separating ON2010 from other strains is not to scale and the length is shown. C), neighbor-joining tree based on the number of alleles that differ between any two strains. D), neighbor-joining tree based on the number of alleles that have none-zero DNA distance between any two strains. Unlike in C, small indels, including possible homopolymer sequencing errors, were not considered in D.