Efficient computation of genotype probabilities for loci with many alleles : II. Iterative method for large, complex pedigrees

An algorithm for computing genotype probabilities for marker loci with many alleles in large, complex pedigrees with missing marker data is pre- sented. The algorithm can also be used to calculate grandparental origin probabilities, which summarize the segregation pattern and are useful for mapping quantitative trait loci. The algorithm is iterative and is based on peeling on alleles instead of the traditional peeling on genotypes. This makes the algorithm more computationally efficient for loci with many alleles. The algorithm is approximate in pedigrees that contain