1. A method of associating a phenotype with one or more candidate chromosomal regions in a genome of a species using a phenotypic data structure that comprises a difference in said phenotype between different strains of said species, said genome including a plurality of loci, said method comprising: establishing a genotypic data structure using a suitably programmed computer, said genotypic data structure corresponding to a locus in said plurality of loci, said genotypic data structure comprising a variation of at least one component of said locus between different strains of said species; determining a correlation value for said genotypic data structure by a comparison of said phenotypic data structure with said genotypic data structure using a suitably programmed computer; repeating said establishing and determining steps for each locus in said plurality of loci using a suitably programmed computer, thereby establishing a plurality of genotypic data structures and, for each respective genotypic data structure in the plurality of genotypic data structures, a correlation value; identifying one or more genotypic data structures in said plurality of genotypic data structures that have correlation values that are higher than the correlation values for all other genotypic data structures in said plurality of genotypic data structures using a suitably programmed computer; wherein the loci that correspond to said one or more genotypic data structures represent said one or more candidate chromosomal regions that associate with said phenotype and wherein an amount of said genome that is included in each locus in said plurality of loci is predetermined at a time prior to said identifying step; wherein each respective genotypic data structure in said plurality of genotypic data structures comprises a plurality of elements and each element in each respective genotypic data structure in said plurality of genotypic data structures corresponds to a difference of at least one component of said locus corresponding to the respective genotypic data structure; wherein, for each element in each respective genotypic data structure in said plurality of genotypic data structures, said different strains of said species are selected from a plurality of strains of said species; wherein an amount that a variation contributes to said at least one component of a locus corresponding to a genotypic data structure in said plurality of genotypic data structures is a function of a distance said variation is away from a center of the locus; and wherein a genotypic data structure in said plurality of genotypic data structures comprises a plurality of variations that are distributed about the center of a locus corresponding to the genotypic data structure, and said establishing step further comprises: fitting a distribution of said plurality of variations about the center of said locus with a probability function; and weighting each variation by a corresponding value derived from said probability function such that variations further from the center of said locus are downweighted so that they contribute less to said genotypic data structure than variations that are closer to said center of said locus; and communicating said one or more genotypic data structures to a user, a display, a readily accessible computer memory or other computer on a network.