A hidden Markov model for detecting segments of shared ancestry (identity by descent) in genetic sequence data.


The program hmmIBD implements a hidden Markov model (HMM) for detecting genomic regions that are identical by descent (IBD) for pairs of haploid samples. It was written to find large IBD regions in sequenced haploid P. falciparum genomes, but it can be applied to other organisms (including phased diploids) and can find shorter IBD regions as well. The program

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