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bioRxiv · 10.1101/057711

RADpainter and fineRADstructure: population inference from RADseq data

Milan Malinsky·Emiliano Trucchi·Daniel Lawson·Daniel Falush
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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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Milan Malinsky, Emiliano Trucchi, Daniel Lawson, Daniel Falush. 2016-06-07. RADpainter and fineRADstructure: population inference from RADseq data. https://doi.org/10.1101/057711

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