Local phylogenetic tree. The compatible intervals and haplotype coloring are shown for a small region. A local phylogeny tree is also shown for the highlighted interval (denoted by the vertical red bar along the compatible interval track). The local phylogeny tree visualization includes the tree structure, size and location annotation for the interval the tree covers, the leaf descriptions including the strains in each leaf, and the distance matrix used to perform the neighbor-joining between leaves. Letters at the leaves of the phylogeny tree denote nodes that contain strains. The leaf descriptions show the corresponding node letter, a confidence score, and number of supporting SNPs along with the set of strains in that leaf. Each strain is colored according to its assigned subspecific origin within the tree's interval and the strains in the currently selected subset are shown as bold to allow the user to quickly identify them.