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  "Title": "Identity by Descent Probability in Pedigrees",
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  "Description": "Identity by Descent (IBD) distributions in pedigrees. A\nHidden Markov Model is used to compute identity coefficients,\nsimulate IBD segments and to derive the distribution of total\nIBD sharing and segment count across chromosomes. The methods\nare applied in Kruijver (2025) <doi:10.3390/genes16050492>. The\nprobability that the total IBD sharing is zero can be computed\nusing the method of Donnelly (1983)\n<doi:10.1016/0040-5809(83)90004-7>.",
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  "Date/Publication": "2025-04-28 09:38:35 UTC",
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      "title": "Probability function for IBD Distribution Objects",
      "topics": [
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      "title": "Compute probability of IBD for pedigree members",
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