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

Phylogenomics of Phrynosomatid Lizards: Conflicting Signals from Sequence Capture versus Restriction Site Associated DNA Sequencing

(2015) Adam D. Leaché et al.   Genome Biology and Evolution

Reconstructing ancient genomes and epigenomes

(2015) Ludovic Orlando et al.   NATURE REVIEWS GENETICS

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

(2014) Deren A. R. Eaton   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Anil Raj et al.   GENETICS

Empirical Assessment of RAD Sequencing for Interspecific Phylogeny

(2014) Astrid Cruaud et al.   MOLECULAR BIOLOGY AND EVOLUTION

Demystifying the RAD fad

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

Restriction site-associated DNA sequencing, genotyping error estimation andde novoassembly optimization for population genetic inference

(2014) A. Mastretta-Yanes et al.   Molecular Ecology Resources

Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

(2014) Brant C. Faircloth et al.   Molecular Ecology Resources

Sequencing Degraded DNA from Non-Destructively Sampled Museum Specimens for RAD-Tagging and Low-Coverage Shotgun Phylogenetics

(2014) Mandy Man-Ying Tin et al.   PLoS One

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

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

Hybridization Capture Using Short PCR Products Enriches Small Genomes by Capturing Flanking Sequences (CapFlank)

(2014) Kyriakos Tsangaras et al.   PLoS One

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

(2013) Hákon Jónsson et al.   BIOINFORMATICS

Unlocking the vault: next-generation museum population genomics

(2013) Ke Bi et al.   MOLECULAR ECOLOGY

The evolutionary history ofXiphophorusfish and their sexually selected sword: a genome-wide approach using restriction site-associated DNA sequencing

(2013) Julia C. Jones et al.   MOLECULAR ECOLOGY

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

(2013) B. Arnold et al.   MOLECULAR ECOLOGY

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 sequencing and population genomics in non-model organisms

(2013) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

PRICE: Software for the Targeted Assembly of Components of (Meta) Genomic Sequence Data

(2013) J. Graham Ruby et al.   G3-Genes Genomes Genetics

Targeted enrichment strategies for next-generation plant biology

(2012) Richard Cronn et al.   AMERICAN JOURNAL OF BOTANY

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

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

(2012) Mathieu Gautier et al.   MOLECULAR ECOLOGY

Special features of RAD Sequencing data: implications for genotyping

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

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

Deep phylogeographic divergence and cytonuclear discordance in the grasshopper Oedaleus decorus

(2012) Eveline Kindler et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC BIOLOGY

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs

(2011) H. E. L. Lischer et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens

(2011) V. C. Mason et al.   GENOME RESEARCH

Museum genomics: low-cost and high-accuracy genetic data from historical specimens

(2011) KEVIN C. ROWE et al.   Molecular Ecology Resources

Applications of next-generation sequencing to phylogeography and phylogenetics

(2011) John E. McCormack et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

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

DNA Damage in Plant Herbarium Tissue

(2011) Martijn Staats et al.   PLoS One

Comparison of solution-based exome capture methods for next generation sequencing

(2011) Anna-Maija Sulonen et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq

(2009) Iouri Chepelev et al.   NUCLEIC ACIDS RESEARCH

Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA

(2009) Adrian W. Briggs et al.   NUCLEIC ACIDS RESEARCH

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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