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  MSMC and MSMC2: the multiple sequentially markovian coalescent

Schiffels, S., & Wang, K. (2020). MSMC and MSMC2: the multiple sequentially markovian coalescent. In J. Y. Dutheil (Ed.), Statistical population genomics (pp. 147-165). New York, NY: Humana. doi:10.1007/978-1-0716-0199-0_7.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0005-9029-A Version Permalink: http://hdl.handle.net/21.11116/0000-0005-902C-7
Genre: Book Chapter

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shh2504.pdf (Publisher version), 3MB
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 Creators:
Schiffels, Stephan1, Author              
Wang, Ke1, Author              
Affiliations:
1Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2074310              

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Free keywords: Demographic inference, Complete genome sequencing, Phasing, Population structure, Coalescent modelling
 Abstract: The Multiple Sequentially Markovian Coalescent (MSMC) is a population genetic method and software for inferring demographic history and population structure through time from genome sequences. Here we describe the main program MSMC and its successor MSMC2. We go through all the necessary steps of processing genomic data from BAM files all the way to generating plots of inferred population size and separation histories. Some background on the methodology itself is provided, as well as bash scripts and python source code to run the necessary programs. The reader is also referred to community resources such as a mailing list and github repositories for further advice.

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Language(s): eng - English
 Dates: 2020-01-242020
 Publication Status: Published in print
 Pages: 20
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1007/978-1-0716-0199-0_7
Other: shh2504
 Degree: -

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Title: Statistical population genomics
Source Genre: Book
 Creator(s):
Dutheil, Julien Y., Editor
Affiliations:
-
Publ. Info: New York, NY : Humana
Pages: 466 Volume / Issue: - Sequence Number: II.7 Start / End Page: 147 - 165 Identifier: ISBN: 978-1-0716-0199-0
ISBN: 978-1-0716-0198-3
DOI: 10.1007/978-1-0716-0199-0

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Title: Methods in Molecular Biology
  Abbreviation : MIMB
Source Genre: Series
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Affiliations:
Publ. Info: New York, NY : Humana
Pages: - Volume / Issue: 2090 Sequence Number: - Start / End Page: - Identifier: ISSN: 1940-6029
ISSN: 1064-3745