Removing the bad apples: A simple bioinformatic method to improve loci‐recovery in de novo RADseq data for non‐model organisms

Multiple Genetic Trajectories to Extreme Abiotic Stress Adaptation in Arctic Brassicaceae

(2020) Siri Birkeland et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2020) Angel G. Rivera‐Colón 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

Conidae phylogenomics and evolution

(2019) Samuel Abalde et al.   ZOOLOGICA SCRIPTA

Evolving Inversions

(2019) Rui Faria et al.   TRENDS IN ECOLOGY & EVOLUTION

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

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

The conundrum of species delimitation: a genomic perspective on a mitogenetically super-variable butterfly

(2019) Vlad Dincă et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genomic impact of severe population decline in a nomadic songbird

(2019) Ross Crates et al.   PLoS One

ipyrad: Interactive assembly and analysis of RADseq datasets

(2019) Deren A R Eaton et al.   BIOINFORMATICS

Marine connectivity dynamics: clarifying cosmopolitan distributions of marine interstitial invertebrates and the meiofauna paradox

(2018) José Cerca et al.   MARINE BIOLOGY

These aren't the loci you're looking for: Principles of effective SNP filtering for molecular ecologists

(2018) Shannon J. O'Leary et al.   MOLECULAR ECOLOGY

Information Dropout Patterns in Restriction Site Associated DNA Phylogenomics and a Comparison with Multilocus Sanger Data in a Species-Rich Moth Genus

(2018) Kyung Min Lee et al.   SYSTEMATIC BIOLOGY

Finding Evolutionary Processes Hidden in Cryptic Species

(2018) Torsten H. Struck et al.   TRENDS IN ECOLOGY & EVOLUTION

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

(2018) Bruno A. S. de Medeiros et al.   PeerJ

Signatures of human-commensalism in the house sparrow genome

(2018) Mark Ravinet et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow

(2017) M. Ravinet et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets

(2017) Julio Rozas et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2017) Nicolas C Rochette et al.   Nature Protocols

vcfr: a package to manipulate and visualize variant call format data in R

(2016) Brian J. Knaus et al.   Molecular Ecology Resources

Shared and nonshared genomic divergence in parallel ecotypes ofLittorina saxatilisat a local scale

(2015) Mark Ravinet et al.   MOLECULAR ECOLOGY

Phylogenomic Test of the Hypotheses for the Evolutionary Origin of Eukaryotes

(2014) Nicolas C. Rochette et al.   MOLECULAR BIOLOGY AND EVOLUTION

Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences

(2014) Huateng Huang et al.   SYSTEMATIC BIOLOGY

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

(2014) Jonathan B. Puritz et al.   PeerJ

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

(2013) B. Arnold et al.   MOLECULAR ECOLOGY

The effect of RAD allele dropout on the estimation of genetic variation within and between populations

(2012) Mathieu Gautier et al.   MOLECULAR ECOLOGY

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

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

(2011) Thibaut Jombart et al.   BIOINFORMATICS

Phylogenomic analyses unravel annelid evolution

(2011) Torsten H. Struck et al.   NATURE

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

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

Gene Flow and Isolation among Populations of Marine Animals

(2009) Michael E. Hellberg   Annual Review of Ecology Evolution and Systematics

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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