1. A method of analyzing a biological sample comprised of the steps: (a) obtaining a biological sample that contains DNA; (b) amplifying the DNA to produce a product; (c) detecting the product to generate data, where the data can be explained by more than one genotype value; (d) assuming a genotype value which is stored in a nontransient memory; and (e) determining a likelihood using a computer in communication with the memory, where the likelihood is defined as a probability of observing the detected data, and said probability is conditioned on the genotype value and other parameters.