PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

A New Method for Genome-wide Marker Development and Genotyping Holds Great Promise for Molecular Primatology

(2013) Christina M. Bergey et al.   INTERNATIONAL JOURNAL OF PRIMATOLOGY

‘Next generation’ biogeography: towards understanding the drivers of species diversification and persistence

(2013) Christian Lexer et al.   JOURNAL OF BIOGEOGRAPHY

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

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

Identification of SNP markers for inferring phylogeny in temperate bamboos (Poaceae: Bambusoideae) using RAD sequencing

(2013) X. Q. Wang et al.   Molecular Ecology Resources

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

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

Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization

(2013) Marie Cariou et al.   Ecology and Evolution

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

(2012) Z. Chong et al.   BIOINFORMATICS

EggLib: processing, analysis and simulation tools for population genetics and genomics

(2012) Stéphane De Mita et al.   BMC GENETICS

Population genomic signatures of divergent adaptation, gene flow and hybrid speciation in the rapid radiation of Lake Victoria cichlid fishes

(2012) I. Keller et al.   MOLECULAR ECOLOGY

Genome-wide patterns of divergence and gene flow across a butterfly radiation

(2012) Nicola J. Nadeau et al.   MOLECULAR ECOLOGY

Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species

(2012) Kai N. Stölting 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

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

Testing for Ancient Admixture between Closely Related Populations

(2011) Eric Y. Durand et al.   MOLECULAR BIOLOGY AND EVOLUTION

Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads

(2011) Paul D. Etter 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

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Small insertions and deletions (INDELs) in human genomes

(2010) J. M. Mullaney et al.   HUMAN MOLECULAR GENETICS

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Estimation of Nucleotide Diversity, Disequilibrium Coefficients, and Mutation Rates from High-Coverage Genome-Sequencing Projects

(2008) M. Lynch   MOLECULAR BIOLOGY AND EVOLUTION

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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