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MORGAN specifications


Unique identifier OMICS_00205
Alternative names MOnte caRlo Genetic ANalysis, ibd-haplo
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 3.4
Stability Stable
Maintained Yes


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  • person_outline Elizabeth Thompson <>

Publications for MOnte caRlo Genetic ANalysis

MORGAN in publications

PMCID: 5133511
PMID: 27980652
DOI: 10.1186/s12919-016-0046-5

[…] for both rare and common variants., we used a set of 1000 ibd graphs [, ] that had been realized on the 7 pedigrees by the morgan/gl_auto program using the ms-2 subset of snps. using the morgan/ibd_haplo program and ms-3, we found that many of the 17 pairs of individuals share ibd in the range 50 to 75 cm on chromosome 3, and that all pairs gave a strong signal of ibd at 69 cm. to infer ibd […]

PMCID: 4143620
PMID: 25519382
DOI: 10.1186/1753-6561-8-S1-S34

[…] the maximum caco ratio, exceeding a certain threshold, we consider this region for association analysis., to compute the ibd states between pairs of individuals, we use thompson's method [] with ibd_haplo (morgan) [,]. this method uses a continuous-time markov rate matrix to model and estimate ibd states among pairs of individuals, using data at dense snp loci, ignoring the ld structure. […]

PMCID: 3664855
PMID: 23535385
DOI: 10.1534/genetics.113.150029

[…] history (; ; ; ), ibd mapping (; ; ), and heritability analysis in founder populations (; ; )., a variety of methods exist for ibd segment detection. probabilistic methods including beagle ibd (), ibd_haplo (), relate (), ibdld (), and plink () fit a hidden markov model (hmm) for ibd status and determine posterior probabilities of ibd. computation times for these methods scale quadratically […]

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MORGAN institution(s)
Department of Statistics, University of Washington, Seattle, WA, USA
MORGAN funding source(s)
Supported in part by NIH grant GM-46255.

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