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PlantImpute is a tool for genotype imputation. The PlantImpute algorithm uses a hidden Markov model (HMM) to track inheritance specifically in plants. The tool is available from Carl Nettelblad by email. See 'contact'.


Population genetics


  • Operation: Imputation
  • Software interface: Command-line user inteface
  • Language: -
  • Operating system: Linux
  • License: Not stated
  • Cost: -
  • Version name: -
  • Credit: Biotechnology and Biological Sciences Research Council (BBSRC), The Roslin Institute, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), he Swedish Research Council, he Knut and Alice Wallenberg Foundation, the European Research Council, the Röntgen-Ångström Cluster, Stiftelsen Olle Engkvist Byggmästare, Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX).
  • Contact: carl.nettelblad _at_
  • Collection: -


John M. Hickey, Gregor Gorjanc, Rajeev K. Varshney, and Carl Nettelblad "Imputation of Single Nucleotide Polymorphism Genotypes in Biparental, Backcross, and Topcross Populations with a Hidden Markov Model" cropscience, vol. 55, september–october 2015.

Download and documentation

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