Journal
MOLECULAR BIOLOGY AND EVOLUTION
Volume 35, Issue 5, Pages 1284-1290Publisher
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msy023
Keywords
population structure; RAD-seq; inference
Funding
- Medical Research Council [MR/M501608/1]
- Austrian Climate Research Programme [ACRP5-EpiChange-KR12AC5K01286]
- Austrian Science Fund (FWF) [Y661-B16]
- Royal Society grant [WT104125MA]
- Wellcome Trust [WT104125MA, 097677/Z/11/Z]
- Wellcome Trust [097677/Z/11/Z] Funding Source: Wellcome Trust
- MRC [MR/L015080/1] Funding Source: UKRI
- Medical Research Council [MR/L015080/1, MR/M501608/1, MR/M501608/2] Funding Source: researchfish
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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-siteassociated 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.
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