Whole genome phylogeny of Streptococcus uberis isolates. A concatenated alignment of 1,377 core genes of 13 isolates was generated by snpTree . The Phi-test  was conducted on non-overlapping 500 base windows of this alignment. Following a Bonferroni correction, those windows with significant evidence (p < 0.05) of recombination were masked from the alignment and the phylogeny determined by PhyML  using a GTR model estimated gamma distribution and 4 substitution rate categories. 200 bootstrap replicates were conducted. Strains initially recorded as clinical isolates are boxed in red.