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AlphaPhase1.1 is a software package for phasing genotype data which uses long range phasing and haplotype library imputation methodology.

AlphaPhase1.1 replaces the original AlphaPhase and is much faster.

The download folder contains Linux, Windows, and Mac executables as well as the manual and a suite of examples.

The user manual is also available here. Download

The paper describing the method is available here. Download

AlphaPhase is not an explicit imputation program, for imputation it is best to use AlphaImpute. Click here 

Your also welcome to try our Gibbs sampler for estimating effects. Click here