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We have incorporated Ritsert Jansen's MQM method into R/qtl (thanks to Danny Arends and Pjotr Prins).
Citations:
Jansen RC (1993) Interval mapping of multiple quantitative trait loci. Genetics 135: 205-211
Jansen RC (1994) Controlling the type I and type II errors in mapping quantitative trait loci. Genetics 138: 871-881
Jansen RC, Stam P (1994) High resolution of quantitative traits into multiple loci via interval mapping. Genetics 136: 1447-1455
Arends D, Prins P, Jansen RC, Broman KW (2010) R/qtl: High-throughput multiple QTL mapping. Bioinformatics 26: 2990-2992