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RADpainter and fineRADstructure: population inference from RADseq data

View ORCID ProfileMilan Malinsky, View ORCID ProfileEmiliano Trucchi, View ORCID ProfileDaniel John Lawson, Daniel Falush
doi: https://doi.org/10.1101/057711
Milan Malinsky
Zoological Institute, University of Basel, 4051 Basel, SwitzerlandWellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK
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  • For correspondence: millanek@gmail.com danielfalush@googlemail.com
Emiliano Trucchi
Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
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Daniel John Lawson
School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN, UK
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Daniel Falush
Milner Centre for Evolution, University of Bath, Bath, BA2 7AY, UK
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  • For correspondence: millanek@gmail.com danielfalush@googlemail.com
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Abstract

Powerful approaches to inferring recent or current population structure based on nearest neighbour haplotype ‘coancestry’ have so far been inaccessible to users without high quality genome-wide haplotype data. With a boom in non-model organism genomics, there is a pressing need to bring these methods to communities without access to such data. Here we present RADpainter, a new program designed to infer the coancestry matrix from restriction-site-associated DNA sequencing (RADseq) data. We combine this program together with a previously published MCMC clustering algorithm into fineRADstructure - a complete, easy to use, and fast population inference package for RADseq data (https://github.com/millanek/fineRADstructure). Finally, with two example datasets, we illustrate its use, benefits, and robustness to missing RAD alleles in double digest RAD sequencing.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted January 29, 2018.
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RADpainter and fineRADstructure: population inference from RADseq data
Milan Malinsky, Emiliano Trucchi, Daniel John Lawson, Daniel Falush
bioRxiv 057711; doi: https://doi.org/10.1101/057711
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RADpainter and fineRADstructure: population inference from RADseq data
Milan Malinsky, Emiliano Trucchi, Daniel John Lawson, Daniel Falush
bioRxiv 057711; doi: https://doi.org/10.1101/057711

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