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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\u2013trans 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.<\/jats:p><jats:p>Availability: R\/qtl is free and open source multi-platform software for the statistical language R, and is made available under the GPLv3 license. R\/qtl can be installed from http:\/\/www.rqtl.org\/. R\/qtl queries should be directed at the mailing list, see http:\/\/www.rqtl.org\/list\/.<\/jats:p><jats:p>Contact: \u00a0kbroman@biostat.wisc.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq565","type":"journal-article","created":{"date-parts":[[2010,10,22]],"date-time":"2010-10-22T04:14:51Z","timestamp":1287720891000},"page":"2990-2992","source":"Crossref","is-referenced-by-count":394,"title":["R\/qtl: high-throughput multiple QTL mapping"],"prefix":"10.1093","volume":"26","author":[{"given":"Danny","family":"Arends","sequence":"first","affiliation":[{"name":"1 Groningen Bioinformatics Centre, University of Groningen, Groningen, 2Department of Nematology, Wageningen University, Wageningen, The Netherlands and 3Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison, Madison, USA"}]},{"given":"Pjotr","family":"Prins","sequence":"additional","affiliation":[{"name":"1 Groningen Bioinformatics Centre, University of Groningen, Groningen, 2Department of Nematology, Wageningen University, Wageningen, The Netherlands and 3Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison, Madison, USA"},{"name":"1 Groningen Bioinformatics Centre, University of Groningen, Groningen, 2Department of Nematology, Wageningen University, Wageningen, The Netherlands and 3Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison, Madison, USA"}]},{"given":"Ritsert C.","family":"Jansen","sequence":"additional","affiliation":[{"name":"1 Groningen Bioinformatics Centre, University of Groningen, Groningen, 2Department of Nematology, Wageningen University, Wageningen, The Netherlands and 3Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison, Madison, USA"}]},{"given":"Karl W.","family":"Broman","sequence":"additional","affiliation":[{"name":"1 Groningen Bioinformatics Centre, University of Groningen, Groningen, 2Department of Nematology, Wageningen University, Wageningen, The Netherlands and 3Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison, Madison, USA"}]}],"member":"286","published-online":{"date-parts":[[2010,10,21]]},"reference":[{"key":"2023012507524990300_B1","doi-asserted-by":"crossref","first-page":"2275","DOI":"10.1534\/genetics.108.088427","article-title":"Bayesian quantitative trait loci mapping for multiple traits","volume":"179","author":"Banerjee","year":"2008","journal-title":"Genetics"},{"key":"2023012507524990300_B2","doi-asserted-by":"crossref","DOI":"10.1007\/978-0-387-92125-9","volume-title":"A Guide to QTL Mapping with R\/qtl.","author":"Broman","year":"2009"},{"key":"2023012507524990300_B3","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1093\/bioinformatics\/btg112","article-title":"R\/qtl: QTL mapping in experimental crosses","volume":"19","author":"Broman","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012507524990300_B4","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1007\/s10519-008-9243-y","article-title":"Evidence for epigenetic interactions for loci on mouse chromosome 1 regulating open field activity","volume":"39","author":"de Mooij-van Malsen","year":"2009","journal-title":"Behav. 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