A known genetic linkage map will be required for the analysis. A good genetic linkage map will comprise a set of Mendelian marker loci that are evenly spaced and span the genome. Average intermarker distances of 5 to 10 centimorgans would be optimal. We have provided ways to simulate linkage maps as well as to convert linkage map information into a format suitable for QTL Cartographer. Presently the user has two options for genetic linkage map input. The first is a format designed for the QTL Cartographer system that allows for free annotation of the data file. An example is given in (6.1.2). A second option allows the user to import the results of a Mapmaker/EXP session. This is covered in more detail in (2.1) and (5.8.1).