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A tool for genotype imputation and phasing. The AlphaImpute algorithm requires pedigree data and couples the long-range phasing with a segregation analysis and haplotype library imputation (SAHLI). The tool is available via email from the Authors.


Population genetics


  • Operation: Imputation
  • Software interface: Command-line user interface
  • Language: Fortran 95
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Other
  • Cost: Free for non-commercial use
  • Version name: -
  • Maturity: beta
  • Credit: Australian Research Council, Genus Plc, Aviagen LTD, Pfizer
  • Contact: john.hickey _at_
  • Collection: -


Antolín R, Nettelblad C, Gorjanc G, Money D, Hickey JM "A hybrid method for the imputation of genomic data in livestock populations." Genet Sel Evol. 2017 Mar 3;49(1):30.
PMID: 28253858
PMCID: PMC5439152

Hickey JM, Cleveland MA, Maltecca C, Gorjanc G, Gredler B, Kranis A "Genotype imputation to increase sample size in pedigreed populations." Methods Mol Biol. 2013;1019:395-410.
PMID: 23756901

Sun C, Wu XL, Weigel KA, Rosa GJ, Bauck S, Woodward BW, Schnabel RD, Taylor JF, Gianola D "An ensemble-based approach to imputation of moderate-density genotypes for genomic selection with application to Angus cattle." Genet Res (Camb). 2012 Jun;94(3):133-50.
PMID: 22809677

Hickey JM, Kinghorn BP, Tier B, van der Werf JH, Cleveland MA "A phasing and imputation method for pedigreed populations that results in a single-stage genomic evaluation." Genet Sel Evol. 2012 Jun 19;44:9.
PMID: 22462519
PMCID: PMC3378429

Hickey JM, Kranis A "Extending long-range phasing and haplotype library imputation methods to impute genotypes on sex chromosomes." Genet Sel Evol. 2013 Apr 25;45:10.
PMID: 23617460
PMCID: PMC3642030

Bouwman AC, Hickey JM, Calus MP, Veerkamp RF "Imputation of non-genotyped individuals based on genotyped relatives: assessing the imputation accuracy of a real case scenario in dairy cattle." Genet Sel Evol. 2014 Feb 3;46:6
PMID: 24490796
PMCID: PMC3929150

Liu X, Hinney A, Scholz M, Scherag A, Tönjes A, Stumvoll M, Stadler PF, Hebebrand J, Böttcher Y "Indications for potential parent-of-origin effects within the FTO gene." PLoS One. 2015 Mar 20;10(3):e0119206.
PMID: 25793382
PMCID: PMC4368796

Cleveland MA, Hickey JM "Practical implementation of cost-effective genomic selection in commercial pig breeding using imputation." J Anim Sci. 2013 Aug;91(8):3583-92.
PMID: 23736050

Ma P, Brøndum RF, Zhang Q, Lund MS, Su G "Comparison of different methods for imputing genome-wide marker genotypes in Swedish and Finnish Red Cattle." J Dairy Sci. 2013 Jul;96(7):4666-77.
PMID: 23684022

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