Coalescent Simulation with msprime

Coalescent simulation is a fundamental tool in modern population genetics. The msprime library provides unprecedented scalability in terms of both the simulations that can be performed and the efficiency with which the results can be processed. We show how coalescent models for population structure...

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Published inMethods in molecular biology Vol. 2090; p. 191
Main Authors Kelleher, Jerome, Lohse, Konrad
Format Journal Article Book Chapter
LanguageEnglish
Published United States 2020
Subjects
Algorithms
Bayes Theorem
Computational Biology - methods
Genetics, Population - methods
Models, Genetic
Simulation
Coalescent theory
Population genetics
Python
Online AccessGet full text
ISSN1064-3745
1940-6029
1940-6029
DOI10.1007/978-1-0716-0199-0_9

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Abstract Coalescent simulation is a fundamental tool in modern population genetics. The msprime library provides unprecedented scalability in terms of both the simulations that can be performed and the efficiency with which the results can be processed. We show how coalescent models for population structure and demography can be constructed using a simple Python API, as well as how we can process the results of such simulations to efficiently calculate statistics of interest. We illustrate msprime's flexibility by implementing a simple (but functional) approximate Bayesian computation inference method in just a few tens of lines of code.
AbstractList Coalescent simulation is a fundamental tool in modern population genetics. The msprime library provides unprecedented scalability in terms of both the simulations that can be performed and the efficiency with which the results can be processed. We show how coalescent models for population structure and demography can be constructed using a simple Python API, as well as how we can process the results of such simulations to efficiently calculate statistics of interest. We illustrate msprime's flexibility by implementing a simple (but functional) approximate Bayesian computation inference method in just a few tens of lines of code.
Author Kelleher, Jerome
Lohse, Konrad
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  givenname: Konrad
  surname: Lohse
  fullname: Lohse, Konrad
  organization: Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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Coalescent theory
Population genetics
Python
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Snippet Coalescent simulation is a fundamental tool in modern population genetics. The msprime library provides unprecedented scalability in terms of both the...
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StartPage 191
SubjectTerms Algorithms
Bayes Theorem
Computational Biology - methods
Genetics, Population - methods
Models, Genetic
Title Coalescent Simulation with msprime
URI https://www.ncbi.nlm.nih.gov/pubmed/31975169
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