This chapter addresses the haplotyping problem for both a single individual and a set of individuals (a population). In the former case the input is haplotype data inconsistent with the existence of exactly two parents for an individual. This inconsistency is due to experimental errors and/or missing data. In the latter case the input data specify for each single nucleotide polymorphism (SNP) and each individual in a population whether her parents have contributed the same or different alleles, but do not specify which parent contributed which allele. The chapter also addresses some of the most interesting combinatorial haplotyping models proposed in the literature. Each model and objective function has specific biological motivations, which are discussed in chapter. The statistical approach has led to widely used software tools for haplotyping, such as the program PHASE. The chapter describes procedure that Clark proposed for haplotyping a population.
