Importance sampling for the infinite sites model

Statistical Applications in Genetics and Molecular Biology
Asger HobolthCarsten Wiuf

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).

References

Jan 1, 1987·Journal of Mathematical Biology·F M Hoppe
Mar 1, 1972·Theoretical Population Biology·S Karlin, J McGregor
Mar 1, 1972·Theoretical Population Biology·W J Ewens
Oct 1, 1995·Theoretical Population Biology·Y X Fu
Nov 2, 1999·Theoretical Population Biology·C Wiuf, P Donnelly
May 4, 2000·Theoretical Population Biology·M Stephens
Oct 20, 2006·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Yun S SongJotun Hein

❮ Previous
Next ❯

Citations

Apr 18, 2009·Theoretical Population Biology·Ganeshkumar Ganapathy, Marcy K Uyenoyama
Mar 3, 2009·Theoretical Population Biology·Asger Hobolth, Carsten Wiuf
Feb 8, 2011·Theoretical Population Biology·Matthias BirknerMatthias Steinrücken
Oct 30, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Yufeng Wu
Oct 8, 2016·Theoretical Population Biology·C MerleP Pudlo
Sep 13, 2019·Genetics·Julia A PalaciosSohini Ramachandran
Mar 1, 2015·Bioinformatics·Kyung-Ah SohnJu Han Kim
Jul 27, 2018·Theoretical Population Biology·Raazesh Sainudiin, Amandine Véber
Nov 1, 2019·Genetics·Julia A PalaciosSohini Ramachandran

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.