R/qtl: high throughput Multiple QTL mapping

D. Arends, J.C.P. Prins, R.C. Jansen, K. Broman

Research output: Contribution to journalArticleAcademicpeer-review

197 Citations (Scopus)


R/qtl is free and powerful software for mapping and exploring quantitative trait loci (QTL). R/qtl provides a fully comprehensive range of methods for a wide range of experimental cross types. We recently added multiple QTL mapping (MQM) to R/qtl. MQM adds higher statistical power to detect and disentangle the effects of multiple linked and unlinked QTL compared with many other methods. MQM for R/qtl adds many new features including improved handling of missing data, analysis of 10 000 s of molecular traits, permutation for determining significance thresholds for QTL and QTL hot spots, and visualizations for cis–trans and QTL interaction effects. MQM for R/qtl is the first free and open source implementation of MQM that is multi-platform, scalable and suitable for automated procedures and large genetical genomics datasets.
Original languageEnglish
Pages (from-to)2990-2992
Issue number23
Publication statusPublished - 2010


  • quantitative trait loci
  • experimental crosses

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