IBDmap is the factorial HMM based algorithm.Several models are supported in this implementation, including both the standard model and the 4-track model which uses a first order Markovian model for the LD process in a subset of the founders.
Laboratory of Computational Biology at the Technion.
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Bioinformatics. 2010 Jun 15;26(12):i175-82. doi: 10.1093/bioinformatics/btq204.
Estimating genome-wide IBD sharing from SNP data via an efficient hidden Markov model of LD with application to gene mapping.
Bercovici S, Meek C, Wexler Y, Geiger D.