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The wgaim (whole genome average interval mapping) package developed in the R system for statistical computing (R Development Core Team 2011) builds on linear mixed modelling techniques by incorporating a whole genome approach to detecting significant quantitative trait loci (QTL) in bi-parental populations. Much of the sophistication is inherited through the well established linear mixed modelling package ASReml-R (Butler et al. 2009). As wgaim uses an extension of interval mapping to incorporate the whole genome into the analysis, functions are provided which allow conversion of genetic data objects created with the qtl package of Broman and Wu (2010) available in R. Results of QTL analyses are available using summary and print methods as well as diagnostic summaries of the selection method. In addition, the package features a flexible linkage map plotting function that can be easily manipulated to provide an aesthetic viewable genetic map. As a visual summary, QTL obtained from one or more models can also be added to the linkage map.