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A tool for genotype imputation for non-model organisms. The LinkImpute algorithm works on unphased data from heterozygous species. It uses the k-nearest neighbor genotype imputation technique (LD-kNNi) and does not require physical or genetic maps. LinkImpute is available in two versions, Java and as an R package. Other names: LinkImputeR.


Population genetics


  • Operation: Imputation
  • Software interface: Command-line user interface; Library
  • Language: Java,R
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: GNU General Public License v3
  • Cost: Free
  • Version name: 1.1.4
  • Maturity: Stable
  • Credit: Genome Canada Bioinformatics and Computational Biology grant, the Canada Research Chairs program, the National Sciences and Engineering Research Council of Canada.
  • Contact: _at_
  • Collection: -


Money D, Gardner K, Migicovsky Z, Schwaninger H, Zhong GY, Myles S "LinkImpute: Fast and Accurate Genotype Imputation for Nonmodel Organisms." G3 (Bethesda). 2015 Sep 15;5(11):2383-90.
PMID: 26377960
PMCID: PMC4632058

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