Whole-genome amplification in double-digest RADseq results in adequate libraries but fewer sequenced loci

lmerTest Package: Tests in Linear Mixed Effects Models

(2017) Alexandra Kuznetsova et al.   Journal of Statistical Software

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

Responsible RAD: Striving for best practices in population genomic studies of adaptation

(2017) David B. Lowry et al.   Molecular Ecology Resources

Polygyny does not explain the superior competitive ability of dominant ant associates in the African ant-plant, Acacia (Vachellia ) drepanolobium

(2017) John H. Boyle et al.   Ecology and Evolution

Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimens

(2017) Ethan B. Linck et al.   Ecology and Evolution

RADseq dataset with 90% missing data fully resolves recent radiation of Petalidium (Acanthaceae) in the ultra-arid deserts of Namibia

(2017) Erin A. Tripp et al.   Ecology and Evolution

Whole Genome Amplification and Reduced-Representation Genome Sequencing of Schistosoma japonicum Miracidia

(2017) Jonathan A. Shortt et al.   PLoS Neglected Tropical Diseases

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

ddRAD-seq phylogenetics based on nucleotide, indel, and presence–absence polymorphisms: Analyses of two avian genera with contrasting histories

(2016) Jeffrey M. DaCosta et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Harnessing the power of RADseq for ecological and evolutionary genomics

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

Extending multivariate distance matrix regression with an effect size measure and the asymptotic null distribution of the test statistic

(2016) Daniel B. McArtor et al.   PSYCHOMETRIKA

Misconceptions on Missing Data in RAD-seq Phylogenetics with a Deep-scale Example from Flowering Plants

(2016) Deren A. R. Eaton et al.   SYSTEMATIC BIOLOGY

Hybridization Capture Using RAD Probes (hyRAD), a New Tool for Performing Genomic Analyses on Collection Specimens

(2016) Tomasz Suchan et al.   PLoS One

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

Assessing the utility of whole genome amplified DNA for next-generation molecular ecology

(2015) Christopher Blair et al.   Molecular Ecology Resources

Impacts of degraded DNA on restriction enzyme associated DNA sequencing (RADSeq)

(2015) Carly F. Graham et al.   Molecular Ecology Resources

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

(2014) Deren A. R. Eaton   BIOINFORMATICS

fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets

(2014) Anil Raj et al.   GENETICS

Population-Genetic Inference from Pooled-Sequencing Data

(2014) Michael Lynch et al.   Genome Biology and Evolution

Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

Amplification Biases and Consistent Recovery of Loci in a Double-Digest RAD-seq Protocol

(2014) Jeffrey M. DaCosta et al.   PLoS One

DISENTANGLING THE EFFECTS OF GEOGRAPHIC AND ECOLOGICAL ISOLATION ON GENETIC DIFFERENTIATION

(2013) Gideon S. Bradburd et al.   EVOLUTION

Estimating and interpreting FST: The impact of rare variants

(2013) G. Bhatia et al.   GENOME RESEARCH

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

(2013) Mathieu Gautier et al.   MOLECULAR ECOLOGY

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

(2013) Robert J. Toonen et al.   PeerJ

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

(2012) N. Rohland et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Inferring Phylogenies from RAD Sequence Data

(2012) Benjamin E. R. Rubin et al.   PLoS One

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

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data

(2011) Thibaut Jombart et al.   BIOINFORMATICS

Discriminant analysis of principal components: a new method for the analysis of genetically structured populations

(2010) Thibaut Jombart et al.   BMC GENETICS

To Pool, or Not to Pool?

(2010) David J. Cutler et al.   GENETICS

Resolving postglacial phylogeography using high-throughput sequencing

(2010) K. J. Emerson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS