Comparison of Parsnp and Comas et al. result on M. tuberculosis dataset. A Venn diagram displays SNPs unique to Comas et al.  (left, blue), unique to Parsnp (right, red), and shared between the two analyses (middle, brown). On top, an unrooted reference phylogeny is given based on the intersection of shared SNPs produced by both methods (90,295 SNPs). On bottom, the phylogenies of Comas et al. (left) and Parsnp (right) are given. Pairs of trees are annotated with their Robinson-Foulds distance (RFD) and percentage of shared splits. The Comas et al. and Parsnp trees are largely concordant with each other and the reference phylogeny. All major clades are shared and well supported by all three trees.