General description

AlphaPeel is a software package for calling, phasing, and imputing genotype and sequence data in pedigree populations. This program implements single locus peeling, multi locus peeling, and hybrid peeling. A complete description of these methods is given in Hybrid peeling for fast and accurate calling, phasing, and imputation with sequence data of any coverage in pedigrees, Genetics Selection Evolution. 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

AlphaPeel is part of a suite of software that our group has developed for imputation. It is fully and freely available to all academics. User are however requested to credit its use on any publications. However, due to our contractual obligations with some of funders of the research program that has developed this suite of software all commercial organisations that wish to use it are requested to contact John Hickey ( to discuss the terms under which it can be used.


1. User Manual

Click here to see the pdf version.

2. Binaries for Linux, Mac and Windows

The AlphaPeel folders contains windows, linux, and mac os executable files, along with an example folder which contains a sample spec file and pipeline for performing hybrid peeling with sequence data.

3. AlphaPeel v0.1.0 (December 2017)

AlphaPeel version v0.1.0 is an early beta version of the code. Please report any bugs or errors to or



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