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
Requirements Snowfall, RcppArmadillo
Source code URL https://cran.r-project.org/src/contrib/hsphase_2.0.1.tar.gz
Maintained Yes



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  • person_outline Mohammad Ferdosi <>

hsphase articles

hsphase citation

PMCID: 4558911

[…] minimum stack depth (m) = 30; distance between stacks (m) = 2; distance between catalog loci (n) = 1., parentage assignment was performed with vitassign v8-5.1 [29] using 200 snps and with r/hsphase using all discovered snps and allowing for a maximum genotyping error of 3 % [30]. r v.3.0.1 was used for chi-square tests to detect significant deviations from the equal sex ratio […]

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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