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Pedihaplotyper is a tool to assign ‘haploblock alleles’ to individuals in a pedigree. A haploblock is a set of closely linked genetic markers among which (almost) no recombination occurs over the pedigree. While the markers are often bi-allelic, a haploblock is usually multi-allelic. Haploblocks therefore summarize the information that is present in separate markers in a form that is much easier to understand for the human investigator, and that allows a much faster (QTL) analysis, requiring less memory resources and with a higher power. While assigning haploblock alleles, PediHaplotyper also resolves conflicting marker data and imputes missing data.

PediHaplotyper requires as input a pedigree, a genetic linkage map of the markers indicating which markers belong to which haploblock, and phased marker data. It can import these data from tab-separated text files and it also can read directly files produced by FlexQTL. The output is again in the form of tab-separated text files, or in a form that can directly be imported by FlexQTL. Also import files for Pedimap are produced for visualizing the results, both in terms of markers and as haploblocks.

PediHaplotyper is an R package; it can be installed from GitHub.


PediHaplotyper is distributed free of charge under the GNU General Public License.


The European project FruitBreedomics (265582-EC-GA) and the USDA-NIFA-SCRI project RosBREED: Enabling marker-assisted breeding in Rosaceae (2009-51181-05808;