Species delineation with Mash

In combination with the species-specific threshold values, we sought to represent Mash’s ability to delineate between bacterial species within the same genus. For this analysis, we ran Mash on the Neisseria and Haemophilus genomes within the reference collection, and used those results to generate neighbor-joining [23] trees. These trees were generated by formatting the Mash results as distance matrices, parsing each matrix and creating the tree with a custom python script built with the BioPython [24] and Phylo [25] packages. The final trees were visualized using the iTOL [26] package.