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R/qtl | QTL mapping in experimental crosses


Allows users to map quantitative trait loci (QTL) in experimental crosses. R/qtl is a comprehensive QTL mapping toolbox for the analysis of experimental populations. The software provides several methods for various experimental cross types. It includes permutation strategies for determining thresholds of significance relevant for QTL and QTL hot spots.

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R/qtl classification

R/qtl specifications

Unique identifier:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
GNU General Public License version 3.0, GNU General Public License version 2.0
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R/qtl distribution


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R/qtl support



  • Karl W. Broman <>

Additional information

Homepage: Tutorials:


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Groningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands; Department of Nematology, Wageningen University, Wageningen, The Netherlands; Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA

Funding source(s)

Supported by National Institutes of Health (GM074244), the Netherlands Organisation for Scientific Research/TTI Green Genetics (1CC029RP), the Centre for BioSystems Genomics (CBSG), the Netherlands Consortium of Systems Biology (NCSB), both of which are part of the Netherlands Genomics Initiative / Netherlands Organisation for Scientific Research and the EU 7th Framework Programme under the Research Project PANACEA (222936).

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