R package lmem.qtler. Performs QTL mapping analysis for balanced and for multi-environment and multi-trait analysis using mixed models. Balanced population, single trait, single environment QTL mapping is performed through marker-regression (Haley and Knott (1992) &lt;<a href=”http://dx.doi.org/10.1038/hdy.1992.131”>doi:10.1038/hdy.1992.131</a>&gt;, Martinez and Curnow (1992) &lt;<a href=”http://dx.doi.org/10.1007/BF00222330”>doi:10.1007/BF00222330</a>&gt;, while multi-environment and multi-trait QTL mapping is performed through linear mixed models. These functions could use any of the following populations: double haploid, F2, recombinant inbred lines, back-cross, and 4-way crosses. Performs a Single Marker Analysis, a Single Interval Mapping, or a Composite Interval Mapping analysis, and then constructs a final model with all of the relevant QTL.