ipyrad: Interactive assembly and analysis of RADseq datasets

Minor allele frequency thresholds strongly affect population structure inference with genomic datasets

(2019) Ethan Linck et al.   Molecular Ecology Resources

Causes and analytical impacts of missing data in RADseq phylogenetics: Insights from an African frog (Afrixalus )

(2019) Marco Crotti et al.   ZOOLOGICA SCRIPTA

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

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

RADseq as a valuable tool for plants with large genomes—A case study in cycads

(2019) James A. R. Clugston et al.   Molecular Ecology Resources

A topoclimate model for Quaternary insular speciation

(2019) Víctor García‐Olivares et al.   JOURNAL OF BIOGEOGRAPHY

Adapterama I: universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext)

(2019) Travis C. Glenn et al.   PeerJ

Practical considerations for plant phylogenomics

(2018) Michael R. McKain et al.   Applications in Plant Sciences

BsRADseq: screening DNA methylation in natural populations of non-model species

(2016) Emiliano Trucchi et al.   MOLECULAR ECOLOGY

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

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

Harnessing the power of RADseq for ecological and evolutionary genomics

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

Comparative genomics reveals convergent rates of evolution in ant–plant mutualisms

(2016) Benjamin E. R. Rubin et al.   Nature Communications

Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference

(2016) Aaron B. A. Shafer et al.   Methods in Ecology and Evolution

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

EpiRADseq: scalable analysis of genomewide patterns of methylation using next-generation sequencing

(2015) Drew R. Schield et al.   Methods in Ecology and Evolution

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

(2014) Deren A. R. Eaton   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

A Framework Phylogeny of the American Oak Clade Based on Sequenced RAD Data

(2014) Andrew L. Hipp et al.   PLoS One

Mapping the sex determination locus in the Atlantic halibut (Hippoglossus hippoglossus) using RAD sequencing

(2013) Christos Palaiokostas et al.   BMC GENOMICS

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae)

(2013) Deren A. R. Eaton et al.   SYSTEMATIC BIOLOGY

Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

(2012) Catherine E. Wagner et al.   MOLECULAR ECOLOGY

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

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

(2012) Joseph K. Pickrell et al.   PLoS Genetics

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

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

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

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

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

Genome resequencing and genetic variation

(2008) Michael Stratton   NATURE BIOTECHNOLOGY

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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