Simulation with RADinitio improves RADseq experimental design and sheds light on sources of missing data

An empirical pipeline for choosing the optimal clustering threshold in RAD seq studies

(2019) Evan McCartney‐Melstad et al.   Molecular Ecology Resources

Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers

(2019) Sean Stankowski et al.   PLOS BIOLOGY

Stacks 2: analytical methods for paired‐end sequencing improve RADseq‐based population genomics

(2019) Nicolas C. Rochette et al.   MOLECULAR ECOLOGY

Adapterama III: Quadruple-indexed, double/triple-enzyme RADseq libraries (2RAD/3RAD)

(2019) Natalia J. Bayona-Vásquez et al.   PeerJ

ipyrad: Interactive assembly and analysis of RADseq datasets

(2019) Deren A R Eaton et al.   BIOINFORMATICS

Signatures of local adaptation along environmental gradients in a range-expanding damselfly (Ischnura elegans )

(2018) Rachael Y. Dudaniec et al.   MOLECULAR ECOLOGY

Genomic signals of selection predict climate-driven population declines in a migratory bird

(2018) Rachael A. Bay et al.   SCIENCE

Would an RRS by any other name sound as RAD?

(2018) Erin O. Campbell et al.   Methods in Ecology and Evolution

A High-Density Integrated DArTseq SNP-Based Genetic Map of Pisum fulvum and Identification of QTLs Controlling Rust Resistance

(2018) Eleonora Barilli et al.   Frontiers in Plant Science

The grayling genome reveals selection on gene expression regulation after whole genome duplication

(2018) Srinidhi Varadharajan et al.   Genome Biology and Evolution

The Arctic charr (Salvelinus alpinus) genome and transcriptome assembly

(2018) Kris A. Christensen et al.   PLoS One

Expanded functionality, increased accuracy, and enhanced speed in the de novo genotyping-by-sequencing pipeline GBS-SNP-CROP

(2018) Arthur T O Melo et al.   BIOINFORMATICS

SLiM 3: Forward Genetic Simulations Beyond the Wright–Fisher Model

(2018) Benjamin C Haller et al.   MOLECULAR BIOLOGY AND EVOLUTION

Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes

(2018) Benjamin C. Haller et al.   Molecular Ecology Resources

quaddRAD: a new high-multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage

(2017) Paolo Franchini et al.   MOLECULAR ECOLOGY

ddrage : A data set generator to evaluate ddRADseq analysis software

(2017) Henning Timm et al.   Molecular Ecology Resources

RADseq provides unprecedented insights into molecular ecology and evolutionary genetics: comment on Breaking RAD by Lowry et al . (2016)

(2017) Garrett J. McKinney et al.   Molecular Ecology Resources

Unbroken: RADseq remains a powerful tool for understanding the genetics of adaptation in natural populations

(2017) Julian M. Catchen et al.   Molecular Ecology Resources

Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: The fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study

(2017) Tomasz Suchan et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Deriving genotypes from RAD-seq short-read data using Stacks

(2017) Nicolas C Rochette et al.   Nature Protocols

RAD sequencing reveals genomewide divergence between independent invasions of the European green crab (Carcinus maenas ) in the Northwest Atlantic

(2017) Nicholas W. Jeffery et al.   Ecology and Evolution

Cold Fusion: Massive Karyotype Evolution in the Antarctic Bullhead Notothen Notothenia coriiceps

(2017) Angel Amores et al.   G3-Genes Genomes Genetics

Contrasting effects of environment and genetics generate a continuum of parallel evolution

(2017) Yoel E. Stuart et al.   Nature Ecology & Evolution

ddradseqtools: a software package for in silico simulation and testing of double-digest RADseq experiments

(2016) F. Mora-Márquez et al.   Molecular Ecology Resources

Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation

(2016) David B. Lowry et al.   Molecular Ecology Resources

RADcap: sequence capture of dual-digest RADseq libraries with identifiable duplicates and reduced missing data

(2016) Sandra L. Hoffberg et al.   Molecular Ecology Resources

Species limits, interspecific hybridization and phylogeny in the cryptic land snail complex Pyramidula : The power of RADseq data

(2016) Oihana Razkin et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Atlantic salmon genome provides insights into rediploidization

(2016) Sigbjørn Lien et al.   NATURE

Harnessing the power of RADseq for ecological and evolutionary genomics

(2016) Kimberly R. Andrews et al.   NATURE REVIEWS GENETICS

Full circumpolar migration ensures evolutionary unity in the Emperor penguin

(2016) Robin Cristofari et al.   Nature Communications

Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes

(2016) Jerome Kelleher et al.   PLoS Computational Biology

RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping

(2015) O. A. Ali et al.   GENETICS

Selection and sex-biased dispersal in a coastal shark: the influence of philopatry on adaptive variation

(2015) D. S. Portnoy et al.   MOLECULAR ECOLOGY

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

(2015) Melanie Schirmer et al.   NUCLEIC ACIDS RESEARCH

Computational analysis of stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding

(2015) Katharine Best et al.   Scientific Reports

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

(2014) Deren A. R. Eaton   BIOINFORMATICS

Population genomics of parallel hybrid zones in the mimetic butterflies,H. melpomeneandH. erato

(2014) Nicola J. Nadeau et al.   GENOME RESEARCH

Demystifying the RAD fad

(2014) Jonathan B. Puritz et al.   MOLECULAR ECOLOGY

SimRAD: an R package for simulation-based prediction of the number of loci expected in RADseq and similar genotyping by sequencing approaches

(2014) Olivier Lepais et al.   Molecular Ecology Resources

Defining Loci in Restriction-Based Reduced Representation Genomic Data from Nonmodel Species: Sources of Bias and Diagnostics for Optimal Clustering

(2014) Daniel C. Ilut et al.   Biomed Research International

dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms

(2014) Jonathan B. Puritz et al.   PeerJ

Estimation of population allele frequencies from next-generation sequencing data: pool-versus individual-based genotyping

(2013) Mathieu Gautier et al.   MOLECULAR ECOLOGY

RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling

(2013) B. Arnold et al.   MOLECULAR ECOLOGY

Genotyping-by-sequencing in ecological and conservation genomics

(2013) Shawn R. Narum et al.   MOLECULAR ECOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

ezRAD: a simplified method for genomic genotyping in non-model organisms

(2013) Robert J. Toonen et al.   PeerJ

Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads

(2012) Z. Chong et al.   BIOINFORMATICS

Special features of RAD Sequencing data: implications for genotyping

(2012) John W. Davey et al.   MOLECULAR ECOLOGY

2b-RAD: a simple and flexible method for genome-wide genotyping

(2012) Shi Wang et al.   NATURE METHODS

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Genome Evolution and Meiotic Maps by Massively Parallel DNA Sequencing: Spotted Gar, an Outgroup for the Teleost Genome Duplication

(2011) Angel Amores et al.   GENETICS

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

Stacks : Building and Genotyping Loci De Novo From Short-Read Sequences

(2011) Julian M. Catchen et al.   G3-Genes Genomes Genetics

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One