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parsnp website  

Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection. Parsnp was designed to work in tandem with Gingr, a flexible platform for visualizing genome alignments and phylogenetic trees.

Environment Modules

Run module spider parsnp to find out what environment modules are available for this application.

System Variables

  • HPC_PARSNP_DIR - installation directory
  • HPC_PARSNP_BIN - executable directory
  • HPC_PARSNP_DOC - documentation directory


If you publish research that uses parsnp you have to cite it as follows:

Treangen TJ*, Ondov BD*, Koren S, Phillippy AM: Rapid Core-Genome Alignment and Visualization for Thousands of Microbial Genomes.