Abstract: Methods for applying graph theory techniques in methods to establish multiplexed assay formats for analyzing polymorphic DNAs are provided. These methods are used for designing and carrying out rapid and efficient processes for distinguishing target polymorphic DNA segments on the basis of variations in sequence and/or length. The methods are thus useful in the design of assays for determining identity, ancestry, predisposition to disease, or the presence or absence of a desired trait; genetic linkage analyses (gene mapping); and drug development.