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This chapter describes the methods used in animal models of sleep to dissect the genetic basis of complex traits that is to say, traits in which variation has both environmental and genetic sources, and in which the genetic component consists of multiple genetic loci. Crosses between inbred strains are still the most widely used method for mapping loci involved in complex traits in model organisms. Cross between inbred strains generates genetically identical offspring, with one chromosome from one strain and one from the other. Genetic mapping using inbred strain crosses proceeds by determining where in the genome genetic variation is associated with phenotypic variation. Two difficulties confront in silico mapping: low power and unequal degrees of relatedness between inbred strains. One attempt to deal with the problem of low power in inbred strain analyses is the development of the hybrid mouse diversity panel (HMDP).