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hsphase specifications


Unique identifier OMICS_13145
Name hsphase
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Hsphase requires a map file (name, chromosome and map positions), a genotype data file (numerically coded as 0, 1, 2 for the three genotypes and 9 for missing data) and a pedigree file (individuals and paternal ancestor).
Input format SNP
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, R
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0.1
Stability Stable
Snowfall, RcppArmadillo
Maintained Yes




No version available



  • person_outline Mohammad Ferdosi

Publications for hsphase

hsphase citation


Genome wide association study of body weight in Australian Merino sheep reveals an orthologous region on OAR6 to human and bovine genomic regions affecting height and weight

PMCID: 4536601
PMID: 26272623
DOI: 10.1186/s12711-015-0142-4
call_split See protocol

[…] The hsphase algorithm [] was used to reconstruct haplotypes on OAR6. Since this algorithm relies on a minimum number of individuals in a half-sib family, we opted for a conservative approach and excluded […]

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hsphase institution(s)
The Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, Australia; Hanwoo Experiment Station, National Institute of Animal Science, RDA, Pyeongchang, Korea
hsphase funding source(s)
This work was supported by a grant from the Next-Generation BioGreen 21 Program (No. PJ008196), Rural Development Administration, Republic of Korea and by an Australian Research Council Discovery Project DP130100542.

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