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Authors: Karl W Broman and Hao Wu, with ideas from Gary Churchilland Śaunak Sen and contributions from Danny Arends,Robert Corty, Timothée Flutre, Ritsert Jansen, Pjotr Prins, LarsRönnegård, Rohan Shah, Laura Shannon, Quoc Tran, AaronWolen, and Brian Yandell

R/qtl is an extensible, interactive environment for mappingquantitative trait loci (QTL) in experimental crosses. It isimplemented as an add-on package for the freely available and widelyused statistical language/softwareR.The development of this software as an add-on to R allows us to takeadvantage of the basic mathematical and statistical functions, andpowerful graphics capabilities, that are provided with R. Further, theuser will benefit by the seamless integration of the QTL mappingsoftware into a general statistical analysis program. Our goal is tomake complex QTL mapping methods widely accessible and allow users tofocus on modeling rather than computing.

A key component of computational methods for QTL mapping is the hiddenMarkov model (HMM) technology for dealing with missing genotypedata. We have implemented the main HMM algorithms, with allowance forthe presence of genotyping errors, for backcrosses, intercrosses, andphase-known four-way crosses.

The current version of R/qtl includes facilities for estimatinggenetic maps, identifying genotyping errors, and performing single-QTLgenome scans and two-QTL, two-dimensional genome scans, by intervalmapping (with the EM algorithm), Haley-Knott regression, and multipleimputation. All of this may be done in the presence of covariates(such as sex, age or treatment). One may also fit higher-order QTLmodels by multiple imputation and Haley-Knott regression.

The R/qtl package is free software; you can redistribute it and/ormodify it under the terms of the GNU General Public License,version 3, as published by the Free Software Foundation.

This program is distributed in the hope that it will be useful, butwithout any warranty; without even the implied warranty ofmerchantability or fitness for a particular purpose. See the GNUGeneral Public License for more details.

A copy of the GNU General Public License, version 3, is available athttps://www.r-project.org/Licenses/GPL-3