hmmIBD

hmmIBD is a software tool for identifying decent among pairs of haploid genotypes. i.e., identity by descent. The hmmIBD algorithm uses the Hidden Markov Model (HMM).

Topic

Genotype and phenotype;Machine learning;Phylogeny

Detail

  • Operation: Phylogenetic tree analysis

  • Software interface: Command-line user interface

  • Language: C

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: 2.0.4

  • Credit: Bill and Melinda Gates Foundation, the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services.

  • Input: tab-delimited text file

  • Output: .hmm.tx

  • Contact: Steve Schaffner sfs@broadinstitute.org

  • Collection: -

  • Maturity: Stable

Publications

  • hmmIBD: software to infer pairwise identity by descent between haploid genotypes.
  • Schaffner SF, Taylor AR, Wong W, Wirth DF, Neafsey DE. hmmIBD: software to infer pairwise identity by descent between haploid genotypes. Malar J. 2018 May 15;17(1):196. doi: 10.1186/s12936-018-2349-7. PMID: 29764422; PMCID: PMC5952413.
  • https://doi.org/10.1186/s12936-018-2349-7
  • PMID: 29764422
  • PMC: PMC5952413

Download and documentation

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