Importance sampling for Lambda-coalescents in the infinitely many sites model

Publication type:
Journal article
Metadata:
Autoren
  • Matthias Birkner
  • Jochen Blath
  • Matthias Steinruecken
Autoren-URL
https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000290467600004&DestLinkType=FullRecord&DestApp=WOS_CPL
DOI
10.1016/j.tpb.2011.01.005
Externe Identifier
  • Clarivate Analytics Document Solution ID: 762IC
  • PubMed Identifier: 21296095
ISSN
0040-5809
Ausgabe der Veröffentlichung
4
Zeitschrift
THEORETICAL POPULATION BIOLOGY
Schlüsselwörter
  • Lambda-coalescent
  • Infinitely many sites model
  • Likelihood estimation
  • Importance sampling
  • Population genetics
Paginierung
155 - 173
Datum der Veröffentlichung
2011
Status
Published
Titel
Importance sampling for Lambda-coalescents in the infinitely many sites model
Sub types
  • Article
Ausgabe der Zeitschrift
79

Data source: Web of Science (Lite)

Other metadata sources:
Autoren
  • Matthias Birkner
  • Jochen Blath
  • Matthias Steinrücken
DOI
10.1016/j.tpb.2011.01.005
ISSN
0040-5809
Ausgabe der Veröffentlichung
4
Zeitschrift
Theoretical Population Biology
Sprache
en
Paginierung
155 - 173
Datum der Veröffentlichung
2011
Status
Published
Herausgeber
Elsevier BV
Herausgeber URL
http://dx.doi.org/10.1016/j.tpb.2011.01.005
Datum der Datenerfassung
2019
Titel
Importance sampling for Lambda-coalescents in the infinitely many sites model
Ausgabe der Zeitschrift
79

Data source: Crossref

Abstract
We present and discuss new importance sampling schemes for the approximate computation of the sample probability of observed genetic types in the infinitely many sites model from population genetics. More specifically, we extend the 'classical framework', where genealogies are assumed to be governed by Kingman's coalescent, to the more general class of Lambda-coalescents and develop further Hobolth et al.'s (2008) idea of deriving importance sampling schemes based on 'compressed genetrees'. The resulting schemes extend earlier work by Griffiths and Tavaré (1994), Stephens and Donnelly (2000), Birkner and Blath (2008) and Hobolth et al. (2008). We conclude with a performance comparison of classical and new schemes for Beta- and Kingman coalescents.
Addresses
  • Johannes-Gutenberg-Universität Mainz, Institut für Mathematik, Staudingerweg 9, 55099 Mainz, Germany. birkner@mathematik.uni-mainz.de
Autoren
  • Matthias Birkner
  • Jochen Blath
  • Matthias Steinrücken
DOI
10.1016/j.tpb.2011.01.005
eISSN
1096-0325
Externe Identifier
  • PubMed Identifier: 21296095
  • PubMed Central ID: PMC3085644
Funding acknowledgements
  • NIGMS NIH HHS: R00 GM080099
  • NIGMS NIH HHS: R00 GM080099-04
  • NIGMS NIH HHS: R00-GM080099
  • NIH: R00-GM080099
Open access
false
ISSN
0040-5809
Ausgabe der Veröffentlichung
4
Zeitschrift
Theoretical population biology
Schlüsselwörter
  • Animals
  • Monte Carlo Method
  • Markov Chains
  • Sampling Studies
  • Genetics, Population
  • Evolution, Molecular
  • Gene Frequency
  • Mutation
  • Models, Genetic
Sprache
eng
Medium
Print-Electronic
Online publication date
2011
Paginierung
155 - 173
Datum der Veröffentlichung
2011
Status
Published
Datum der Datenerfassung
2011
Titel
Importance sampling for Lambda-coalescents in the infinitely many sites model.
Sub types
  • Research Support, Non-U.S. Gov't
  • research-article
  • Journal Article
  • Research Support, N.I.H., Extramural
Ausgabe der Zeitschrift
79

Files

https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21296095/pdf/?tool=EBI https://europepmc.org/articles/PMC3085644?pdf=render

Data source: Europe PubMed Central

Abstract
We present and discuss new importance sampling schemes for the approximate computation of the sample probability of observed genetic types in the infinitely many sites model from population genetics. More specifically, we extend the 'classical framework', where genealogies are assumed to be governed by Kingman's coalescent, to the more general class of Lambda-coalescents and develop further Hobolth et al.'s (2008) idea of deriving importance sampling schemes based on 'compressed genetrees'. The resulting schemes extend earlier work by Griffiths and Tavaré (1994), Stephens and Donnelly (2000), Birkner and Blath (2008) and Hobolth et al. (2008). We conclude with a performance comparison of classical and new schemes for Beta- and Kingman coalescents.
Date of acceptance
2011
Autoren
  • Matthias Birkner
  • Jochen Blath
  • Matthias Steinrücken
Autoren-URL
https://www.ncbi.nlm.nih.gov/pubmed/21296095
DOI
10.1016/j.tpb.2011.01.005
eISSN
1096-0325
Externe Identifier
  • NIH Manuscript Submission ID: NIHMS277884
  • PubMed Central ID: PMC3085644
Funding acknowledgements
  • NIGMS NIH HHS: R00 GM080099
  • NIGMS NIH HHS: R00 GM080099-04
  • NIGMS NIH HHS: R00-GM080099
Ausgabe der Veröffentlichung
4
Zeitschrift
Theor Popul Biol
Schlüsselwörter
  • Animals
  • Evolution, Molecular
  • Gene Frequency
  • Genetics, Population
  • Markov Chains
  • Models, Genetic
  • Monte Carlo Method
  • Mutation
  • Sampling Studies
Sprache
eng
Country
United States
Paginierung
155 - 173
PII
S0040-5809(11)00013-X
Datum der Veröffentlichung
2011
Status
Published
Datum, an dem der Datensatz öffentlich gemacht wurde
2011
Titel
Importance sampling for Lambda-coalescents in the infinitely many sites model.
Sub types
  • Journal Article
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
Ausgabe der Zeitschrift
79

Data source: PubMed

Abstract
We present and discuss new importance sampling schemes for the approximate computation of the sample probability of observed genetic types in the infinitely many sites model from population genetics. More specifically, we extend the 'classical framework', where genealogies are assumed to be governed by Kingman's coalescent, to the more general class of Lambda-coalescents and develop further Hobolth et. al.'s (2008) idea of deriving importance sampling schemes based on 'compressed genetrees'. The resulting schemes extend earlier work by Griffiths and Tavar\'e (1994), Stephens and Donnelly (2000), Birkner and Blath (2008) and Hobolth et. al. (2008). We conclude with a performance comparison of classical and new schemes for Beta- and Kingman coalescents.
Autoren
  • Matthias Birkner
  • Jochen Blath
  • Matthias Steinruecken
Autoren-URL
http://arxiv.org/abs/1105.1836v1
Zeitschrift
Theor. Popul. Biol.
Schlüsselwörter
  • math.PR
  • math.PR
  • q-bio.PE
  • 62F99 (Primary) 62P10, 92D10, 92D20 (Secondary)
Notes
(38 pages, 40 figures)
Paginierung
155 - 173
Datum der Veröffentlichung
2011
Herausgeber URL
http://dx.doi.org/10.1016/j.tpb.2011.01.005
Datum der Datenerfassung
2011
Datum, an dem der Datensatz öffentlich gemacht wurde
2011
Titel
Importance sampling for Lambda-coalescents in the infinitely many sites model
Ausgabe der Zeitschrift
79

Files

1105.1836v1.pdf

Data source: arXiv

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