RADpainter and fineRADstructure

Population Inference from RADseq Data

Milan Malinsky, Emiliano Trucchi, Daniel John Lawson, Daniel Falush

Research output: Contribution to journalArticle

20 Citations (Scopus)

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 languageEnglish
Pages (from-to)1284-1290
Number of pages7
JournalMolecular Biology and Evolution
Volume35
Issue number5
Early online date20 Feb 2018
DOIs
Publication statusPublished - 1 May 2018

Fingerprint

DNA Sequence Analysis
Haplotypes
haplotypes
sequence analysis
DNA
Genomics
Population
Cluster Analysis
population structure
Alleles
Genome
alleles
genomics
genome
organisms
allele
matrix
methodology
Datasets
programme

Keywords

  • Inference
  • Population structure
  • RAD-seq

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

Cite this

RADpainter and fineRADstructure : Population Inference from RADseq Data. / Malinsky, Milan; Trucchi, Emiliano; Lawson, Daniel John; Falush, Daniel.

In: Molecular Biology and Evolution, Vol. 35, No. 5, 01.05.2018, p. 1284-1290.

Research output: Contribution to journalArticle

Malinsky, Milan ; Trucchi, Emiliano ; Lawson, Daniel John ; Falush, Daniel. / RADpainter and fineRADstructure : Population Inference from RADseq Data. In: Molecular Biology and Evolution. 2018 ; Vol. 35, No. 5. pp. 1284-1290.
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