Supporting data files for manuscript: 'Australian porcine CC10 E. coli belong to multiple sublineages of a highly diverse global CC10 phylogeny'
EC_customDB.fasta - Custom database of additional genes screened in this study
core.txt - Tab-delimited summary of percentage of bases aligned to reference for all strains
full.core.clean.gubbins.aln - Snippy cleaned, recombination filtered alignment.
full.core.clean.gubbins.snpsites.aln - As above with SNPs identified with snp-sites
full.core.clean.gubbins.snpsites.pairwise_snps.txt - Tab-delimited pairwise SNPs derived from the above alignment
full.core.clean.gubbins.snpsites.tree - Maximum-likelihood tree derived from full.core.clean.gubbins.snpsites.aln
full.core.clean.gubbins.snpsites.rooted.tree - As above, but rooted on HS outgroup strain
snippycore.aln - Core SNP alignment generated by snippy-core
snippycore.tree - Maximum-likelihood tree derived from the above alignment
CC10_MDS.R - R code used for MDS analysis and visualisation
CC10_SNPtree_heatmap.R - R code used to generate supplementary heatmaps