Biostatistics 666: Haplotype Estimation
This lecture introduces several strategies for estimating individual haplotypes and their frequencies. At heart, all population-based haplotyping algorithms look for haplotypes that are shared across multiple individuals. The simplest approach for haplotyping using this information is Clark's 1990 algorithm, which is intuitively simple but quite effective in a variety of settings. The E-M algorithm, which provides an important refinements at the cost of more computation, is also introduced. Further refined methods are also discussed.
Clark (1990) Mol Biol Evol 7:111-122
Excoffier and Slatkin (1995) Mol Biol Evol 12:921-927