General description

AlphaImpute is a software package for imputing and phasing genotype data in populations with pedigree information available. The program uses segregation analysis and haplotype library imputation to impute alleles and genotypes. A complete description of the methods is given in Hickey et al. (2012). AlphaImpute consists of a single program however it calls both AlphaPhase1.1 (Hickey et al., 2011) and GeneProbForAlphaImpute (Kerr and Kinghorn, 1996). All information on the model of analysis, input files and their layout, is specified in a single parameter file.

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Commercial use

AlphaImpute is freely available to academic researchers. Commercial organisations wishing to use AlphaImpute are requested to contact


1. User Manual

Click here to see the pdf version.

2. Binaries for Linux, Mac and Windows

The AlphaImpute folders contains:

  • 1 Executable (and .dlls if on windows)
  • 1 pdf (AlphaImpute User Manual),
  • 1 parameter file (AlphaImputeSpec.txt)
  • 1 folder with a small example containing (Example):
    • 1 parameter file (AlphaImputeSpec.txt)
    • 1 pedigree file (Pedigree.txt)
    • 1 file with the genotype information (Genotypes.txt)
    • 1 file with the true genotype information for all the individuals (TrueGenotypes.txt)
    • 1 file listing the masked genotypes (ListMaskedGenotypes.txt)

Running AlphaImpute requires AlphaImputeSpec.txt.

3. AlphaImpute v1.9.8 (March 2018)

AlphaImpute version 1.9 comes with many bug fixes and improvements.



  1. Fixed issues with some pedigrees

v1.9.8 1/2

  1. Updated AlphaPhase version
  2. Various bug fixes
  3. Improved AlphaImputeSpecUsed.txt output
  4. Allow for plink output


  1. Updated AlphaPhase version
  2. Added default parameters for the spec file
  3. Added new AlphaImputeSpecUsed.txt output showing what options the program has used
  4. Rewritten user manual


  1. Fixed HMM bugs
  2. Improved handling of PLINK files
  3. Added support for .ref files for specifying reference allele
  4. Clarified output


  1. Error checking of pedigree files
  2. Fixed bug when dealing with plink files
  3. fixed alphaphase memory issues


  1. Reduction in unnecessary IO
  2. Support for working directly with binary and text plink files
  3. Speed improvements
  4. Memory management improvements
  5. Support for multiple chromosome


  1. Fixes to Phasing Algorithms
  2. Fixes to output subroutines


  1. Faster bitwise operations
  2. Better accuracy for imputation compared to older versions on certain datasets
  3. Much lower memory requirements
  4. Much better usability
  5. Less usage on disk
  6. Huge overall runtime improvements

Note - the restart options have changed in this version. Please update your pipelines accordingly.

Windows: Download

Mac OS: Download

Linux: Download


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