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HighMap specifications


Unique identifier OMICS_14964
Name HighMap
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained No


No version available


This tool is not maintained anymore.

Publication for HighMap

HighMap citations


High Density Genetic Map Construction and Identification of QTLs Controlling Oleic and Linoleic Acid in Peanut using SLAF seq and SSRs

Sci Rep
PMCID: 5883025
PMID: 29615772
DOI: 10.1038/s41598-018-23873-7

[…] Comparing with the reference genome (http://peanutbase.org/home), HighMap assigned 2,334 of 2,384 markers to 20 LGs of peanut including 2,266 SNPs and 68 SSRs. The total genetic length of the molecular linkage map was 2,586.37 cM in twenty linkage groups with a mean […]


High Density Genetic Map Construction and Stem Total Polysaccharide Content Related QTL Exploration for Chinese Endemic Dendrobium (Orchidaceae)

Front Plant Sci
PMCID: 5880926
PMID: 29636767
DOI: 10.3389/fpls.2018.00398

[…] rtitioning the filtered marker into linkage groups (LGs) based on their locations on the GREEN genome, we used the MLOD scores >5 between markers to confirm the robustness of markers for each LG. The HighMap strategy was utilized to order the SLAF markers and correct genotyping errors within LGs, in order to ensure the efficient construction of a high-density and high-quality map (Liu D.Y. et al., […]


High density genetic map construction and comparative genome analysis in asparagus bean

Sci Rep
PMCID: 5859152
PMID: 29555986
DOI: 10.1038/s41598-018-23173-0

[…] Finally obtained high-quality SNP markers were used for map construction using HighMap software. HighMap consists of four modules, including linkage grouping, marker ordering, error genotyping correction and map evaluation. Firstly, in grouping module, markers were clustered int […]


Improvement of Salt Tolerance Using Wild Rice Genes

Front Plant Sci
PMCID: 5776132
PMID: 29387076
DOI: 10.3389/fpls.2017.02269

[…] ix regions of high density on Chr. 2, 5, 6, 7, 10, and 11 (Figures ).After filtering SLAFs with sequencing depth under 10 × or heterozygous in parents, we obtained 5,479 polymorphic SLAFs. Then using HighMap software (Liu et al., ), we constructed a high density linkage map from SLAF-seq genotyping data of DJ15 × Koshihikari F2:4 lines. After filtering makers with MLOD <5, we arranged 5,472 of 5,4 […]


SLAF based high density genetic map construction and QTL mapping for major economic traits in sea urchin Strongylocentrotus intermedius

Sci Rep
PMCID: 5770408
PMID: 29339742
DOI: 10.1038/s41598-017-18768-y

[…] han five SNP; 3) segregating markers could be genotyped in at most 70% of individuals; 4) markers with significant SD (P < 0.01). The other SLAF markers were used to perform linkage map construction. HighMap software was used to construct the genetic map of sea urchin after linkage grouping according to single-linkage clustering algorithm at the logarithm of odds (LOD) threshold ≥5.0 and a maximum […]


Construction of an SNP based high density linkage map for flax (Linum usitatissimum L.) using specific length amplified fragment sequencing (SLAF seq) technology

PLoS One
PMCID: 5739455
PMID: 29267332
DOI: 10.1371/journal.pone.0189785

[…] 0.001) segregation distortion; 4) SNPs showing less than 70% integrity of individual segregation patterns. To ensure efficient construction of the high-density and high-quality map, a newly developed HighMap [] strategy was utilized to order the SNP markers and correct genotyping errors within LGs. Firstly, recombinant frequencies and MLOD [] scores were calculated by two-point analysis, which wer […]


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HighMap institution(s)
Biomarker Technologies Corporation, Beijing, China; Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China; State Key laboratory of Crop Genetic and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences (IVF, CAAS), Beijing, China
HighMap funding source(s)
This work was supported by a National Program on Key Basic Research Projects (the 973 Program: 2012CB113906 and 2012CB113900), a National High Technology Research and Development Program of China (the 863 Program, No. 2012AA100101).

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