Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees.



  • Parsnp - Core-genome alignment and analysis
  • Gingr - Interactive visualization of alignments, trees and variants
  • HarvestTools - Archiving and postprocessing


Treangen TJ, Ondov BD, Koren S, Phillippy AM. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biology, 15 (11), 1-15 [PDF]

Download (v1.1.2, 24-Mar-2015)