Book section
Coalescent simulation with msprime
- 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.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
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(Preview, Version of record, pdf, 2.2MB, Terms of use)
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- Publisher copy:
- 10.1007/978-1-0716-0199-0_9
Authors
- Publisher:
- Springer
- Host title:
- Statistical Population Genomics
- Journal:
- Statistical Population Genomics More from this journal
- Pages:
- 191-230
- Series:
- Methods in Molecular Biology
- Series number:
- 2090
- Publication date:
- 2020-01-24
- DOI:
- Pmid:
-
31975169
- EISBN:
- 9781071601990
- ISBN:
- 9781071601983
- Language:
-
English
- Keywords:
- Pubs id:
-
1084460
- Local pid:
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pubs:1084460
- Deposit date:
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2020-02-21
- ARK identifier:
Terms of use
- Copyright holder:
- J.Y. Dutheil, J. Kellher, and K. Lohse
- Copyright date:
- 2020
- Rights statement:
- © The Editor(s) (if applicable) and The Author(s) 2020. Open Access: This book is licensed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if changes were made. The images or other third party material in this book are included in the book’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the book’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.
- Licence:
- CC Attribution (CC BY)
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