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Mol Biol Evol. 2018 May 1;35(5):1284-1290. doi: 10.1093/molbev/msy023.

RADpainter and fineRADstructure: Population Inference from RADseq Data.

Author information

1
Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland.
2
Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
3
Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
4
School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom.
5
Milner Centre for Evolution, University of Bath, Bath, United Kingdom.

Abstract

Powerful approaches to inferring recent or current population structure based on nearest neighbor haplotype "coancestry" have so far been inaccessible to users without high quality genome-wide haplotype data. With a boom in nonmodel 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; last accessed February 24, 2018). Finally, with two example data sets, we illustrate its use, benefits, and robustness to missing RAD alleles in double digest RAD sequencing.

PMID:
29474601
PMCID:
PMC5913677
DOI:
10.1093/molbev/msy023
[Indexed for MEDLINE]
Free PMC Article

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