Fig. 7

Virulence factor analyses in SuperPhy. A screen capture showing the matrix representation of all genomes that contain an allele of the eae gene. The matrix contains more data than can be displayed in a single image, but it is interactive and scrollable, allowing the full matrix to be explored by the user. The metadata category ‘Serotype’ has been activated and can be seen as appended to the strain name in the row names of the matrix. The numbers within the matrix indicate the copy number of an allele within a genome, and empty boxes indicate the absence of an allele. The histogram displays the copy number of all genes searched for; in this case, the number of eae alleles