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., 2011) and Haplotype Library Imputation (Hickey et al., 2011). AlphaPhase consists of a single program. All information on the model of analysis, input files and their layout, is specified in a parameter file.
The AlphaPhase.zip file contains executibles for Windows, Linux, and Mac, a manual, and an example dataset.
AlphaPhase is part of a suite of software that our group has developed. It is fully and freely available for all use under the MIT License.
Hickey, J. M., B. P. Kinghorn, B. Tier, J. F. Wilson, N. Dunstan and J. H. van der Werf. 2011. A Combined Long-Range Phasing and Long Haplotype Imputation Method to Impute Phase for SNP Genotypes. Genetics Selection Evolution 43:12.