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Harvest

http://harvest.readthedocs.io/en/latest/index.html

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.

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Tools

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

Citation

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]