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Scoary is a tool to score associations phenotypes to pan-genome components. The Scoary algorithm considers population stratification with the least possible assumptions of evolutionary processes and outputs a list of genes sorted by strength of trait association.


Genotype and phenotype; Model organisms; GWAS study; Functional genomics


  • Operation: Analysis
  • Software interface: Command-line user interface
  • Language: Python
  • Operating system: Linux
  • License: GNU General Public License v3
  • Cost: Free
  • Version name: 1.6.14
  • Maturity: Stable
  • Credit: Norwegian Institute of Public Health (NIPH), the Norwegian Research Council.
  • Contact: ola.brynildsrud _at_ | Vegard Eldholm vegard.eldholm _at_
  • Collection: -


Brynildsrud O, Bohlin J, Scheffer L, Eldholm V "Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary." Genome Biol. 2016; 17(1):238
PMID: 27887642
PMCID: PMC5124306

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