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PlantImpute

PlantImpute

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'.

Topic

Population genetics

Details

  • 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 Rntgen-ngstrm Cluster, Stiftelsen Olle Engkvist Byggmstare, Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX).
  • Contact: carl.nettelblad _at_ icm.uu.se
  • Collection: -

Publications

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, septemberoctober 2015. https://doi.org/10.2135/cropsci2014.09.0648

Download and documentation


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