The locus ordering problem

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Abstract
Studies of phenotypes defined by codominant alleles at two or more loci in three-generation families allow haplotypes to be deduced. These data are easily summarized by the Mendelian convention of upper and lower case, with case defining phase rather than nature. In two-generation families haplotypes may be inferred with high precision for closely linked loci even if an allele at one locus is recessive. Coding procedures are discussed and a simple solution to inferring the most likely order of three or more loci, and defining its likelihood compared with other orders, is presented.

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