IDEAS home Printed from https://ideas.repec.org/a/bpj/sagmbi/v7y2008i1n32.html
   My bibliography  Save this article

Importance Sampling for the Infinite Sites Model

Author

Listed:
  • Hobolth Asger

    (Aarhus University)

  • Uyenoyama Marcy K

    (Duke University)

  • Wiuf Carsten

    (Aarhus University)

Abstract

Importance sampling or Markov Chain Monte Carlo sampling is required for state-of-the-art statistical analysis of population genetics data. The applicability of these sampling-based inference techniques depends crucially on the proposal distribution. In this paper, we discuss importance sampling for the infinite sites model. The infinite sites assumption is attractive because it constraints the number of possible genealogies, thereby allowing for the analysis of larger data sets. We recall the Griffiths-Tavaré and Stephens-Donnelly proposals and emphasize the relation between the latter proposal and exact sampling from the infinite alleles model. We also introduce a new proposal that takes knowledge of the ancestral state into account. The new proposal is derived from a new result on exact sampling from a single site. The methods are illustrated on simulated data sets and the data considered in Griffiths and Tavaré (1994).

Suggested Citation

  • Hobolth Asger & Uyenoyama Marcy K & Wiuf Carsten, 2008. "Importance Sampling for the Infinite Sites Model," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 7(1), pages 1-26, October.
    • Handle: RePEc:bpj:sagmbi:v:7:y:2008:i:1:n:32
    DOI: 10.2202/1544-6115.1400
    as

    Download full text from publisher

    File URL: https://doi.org/10.2202/1544-6115.1400
    Download Restriction: For access to full text, subscription to the journal or payment for the individual article is required.
    File URL: https://libkey.io/10.2202/1544-6115.1400?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Uyenoyama, Marcy K. & Takebayashi, Naoki & Kumagai, Seiji, 2020. "Allele frequency spectra in structured populations: Novel-allele probabilities under the labelled coalescent," Theoretical Population Biology, Elsevier, vol. 133(C), pages 130-140.
    2. Merle, C. & Leblois, R. & Rousset, F. & Pudlo, P., 2017. "Resampling: An improvement of importance sampling in varying population size models," Theoretical Population Biology, Elsevier, vol. 114(C), pages 70-87.
    3. Sainudiin, Raazesh & Véber, Amandine, 2018. "Full likelihood inference from the site frequency spectrum based on the optimal tree resolution," Theoretical Population Biology, Elsevier, vol. 124(C), pages 1-15.
    4. Jenkins Paul A., 2012. "Stopping-Time Resampling and Population Genetic Inference under Coalescent Models," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(1), pages 1-20, January.
    5. Ganapathy, Ganeshkumar & Uyenoyama, Marcy K., 2009. "Site frequency spectra from genomic SNP surveys," Theoretical Population Biology, Elsevier, vol. 75(4), pages 346-354.
    6. Hobolth, Asger & Wiuf, Carsten, 2009. "The genealogy, site frequency spectrum and ages of two nested mutant alleles," Theoretical Population Biology, Elsevier, vol. 75(4), pages 260-265.
    7. Birkner, Matthias & Blath, Jochen & Steinrücken, Matthias, 2011. "Importance sampling for Lambda-coalescents in the infinitely many sites model," Theoretical Population Biology, Elsevier, vol. 79(4), pages 155-173.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:bpj:sagmbi:v:7:y:2008:i:1:n:32. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Peter Golla (email available below). General contact details of provider: https://www.degruyter.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.