A new algorithm for haplotype‐based association analysis: the Stochastic‐EM algorithm

By D. Trégouët, Sylvie Escolano, L. Tiret, Alain Mallet, Jean-Louis Golmard. Annals of Human Genetics, 2004

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Haplotype phasing: Existing methods and new developments (2011, methodology): “In each case, the approximate coalescent gives rise to an HMM, and its parameters are estimated with the use of iterative algorithms, such as the stochastic EM algorith”
Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. (2007, methodology): “The algorithm that we have described is similar to a stochastic EM algorithm 20,21 ; however, our model does not include a likelihood.”