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Haplotag specifications


Unique identifier OMICS_10604
Name Haplotag
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Windows
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Jiro Hattori <>

Publication for Haplotag

Haplotag citations


Tools for Genetic Studies in Experimental Populations of Polyploids

PMCID: 5915555
PMID: 29720992
DOI: 10.3389/fpls.2018.00513

[…] tetraploid data, whilst hapcompass performed best at higher ploidies (6× and higher) (). both shesisplus and tripoly have yet to be independently tested. for allopolyploid species, the user-friendly haplotag software has been designed to identify both single snps and multi-snp haplotypes from genotypes developed using next generation sequencing data (). an interesting feature is the use […]


Phased Genotyping by Sequencing Enhances Analysis of Genetic Diversity and Reveals Divergent Copy Number Variants in Maize

PMCID: 5499125
PMID: 28526729
DOI: 10.1534/g3.117.042036

[…] then multi-nucleotide polymorphisms (mnps) can be genotyped. the use of mnps has not been widely exploited in gbs due to the lack of tools for scoring phased genotypes. the software stacks () and haplotag () do have functions embedded within their pipelines for extracting mnp haplotypes from gbs data, but the pipeline-dependency of these functions limits their use more generally, […]


High density marker profiling confirms ancestral genomes of Avena species and identifies D genome chromosomes of hexaploid oat

PMCID: 5069325
PMID: 27522358
DOI: 10.1007/s00122-016-2762-7

[…] and that this strategy could help to elucidate a more detailed understanding of the ancestral genomes of hexaploid oat. in preparation for this work, we developed a novel gbs pipeline called ‘haplotag’ (tinker et al. ) which was designed to discover and assign tag-level haplotypes to discrete diploid loci in a systematic way using population-level filters. we reasoned that, by identifying […]

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Haplotag institution(s)
Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada

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