These pages provide a guided tour through the main features and quirks of MERLIN. The section on input file formats is recommended for all users. The other sections will depend on the focus of your research. Merlin can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation. Linkage disequilibrium between markers can be accomodated in most analyses.