Identifying segments of the genome that are identical-by-descent (IBD) between individuals is a fundamental concept in genetics. IBD data are used in numerous applications including demographic inference, heritability estimation, and disease loci mapping. Therefore, the identification of IBD segments from genome-wide genotyping studies, and more recently sequencing studies, has important implications for studies of complex human traits. Current methods for detecting IBD fall into two categories: multiway or pair-wise. Multiway methods detect IBD over multiple haplotypes simultaneously and leverage the clique structure of true IBD. Although powerful, these approaches are generally computationally expensive since the number of potential IBD relationships at a locus is O(2~(h(h-1)/2)), where h is the number of haplotypes. As a result, many state-of-the-art methods estimate the probability of IBD between pairs of haplotypes independently. The result is a much more efficient method but at the expense of loss of power when detecting smaller IBD segments (＜1 centimorgans).
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