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R/qtl2 (aka qtl2) is a reimplementation of the QTL analysis software R/qtl, to better handle high-dimensional data and complex cross designs.

Also see the related packages, qtl2convert (for converting data among the R/qtl2, DOQTL, and R/qtl formats), qtl2fst (for storing genotype probabilities on disk), and qtl2ggplot (for ggplot2-based data visualizations).

Discussion group

For discussion/questions about R/qtl2, join the rqtl2-disc google group. Or join rqtl-announce for announcements about R/qtl and R/qtl2. (We’ll try to keep the original rqtl-disc group for the discussion/questions about the original R/qtl only.)


Install R/qtl2 from CRAN:




To cite R/qtl2 in publications, use:

Broman KW, Gatti DM, Simecek P, Furlotte NA, Prins P, Sen Ś, Yandell BS, Churchill GA (2019) R/qtl2: software for mapping quantitative trait loci with high-dimensional data and multi-parent populations. Genetics 211:495-502 doi:10.1534/genetics.118.301595 pdf


Licensed under GPL-3.

Sources on github: