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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.
Original language | English |
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Pages (from-to) | 1284-1290 |
Number of pages | 7 |
Journal | Molecular Biology and Evolution |
Volume | 35 |
Issue number | 5 |
Early online date | 20 Feb 2018 |
DOIs | |
Publication status | Published - 1 May 2018 |
Keywords
- Inference
- Population structure
- RAD-seq
ASJC Scopus subject areas
- Ecology, Evolution, Behavior and Systematics
- Molecular Biology
- Genetics
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Dive into the research topics of 'RADpainter and fineRADstructure: Population Inference from RADseq Data'. Together they form a unique fingerprint.Projects
- 1 Finished
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The MRC Consortium for Microbial Bioinformatics Fellowship 1
Falush, D. (PI)
1/08/16 → 31/07/19
Project: Research council