General description

AlphaPhase is a software package for phasing genotype data. The program implements methods to determine phase using an extended Long Range Phasing (Kong et al., 2008, Hickey et al., 2010) and Haplotype Library Imputation (Hickey et al., 2009 and 2010). AlphaPhase consists of a single program. All information on the model of analysis, input files and their layout, is specified in a parameter file.

Any questions? go to AlphaPhase Forum and join the discussion.

Commercial use

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


1. User Manual

Click here to see the html version.

Or download the pdf using the following link:

2. Binaries for Linux, Mac and Windows

The AlphaPhase1.1 folders contains:

  • 1 binary (AlphaPhase),
  • 1 pdf (AlphaPhase User Manual),
  • 1 parameter file (AlphaPhaseSpec.txt)

Running AlphaPhase requires AlphaPhaseSpec.txt

3. AlphaPhase Version 1.2 (Sep 2016)