Treangen TJ, Ondov BD, Koren S, Phillippy AM.

Genome Biol. 2014;15(11):524.

The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes.

Requires > 97% similarity between genomes. Species with a too low Maximal Unit Match (MUM) index distance are not incorporated in the core genome alignment.