Development, validation and high-throughput analysis of sequence markers in nonmodel species

Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing

(2013) Paul A. Hohenlohe et al.   MOLECULAR ECOLOGY

No evidence for nuclear introgression despite complete mtDNA replacement in the Carpathian newt (Lissotriton montandoni)

(2013) P. Zieliński et al.   MOLECULAR ECOLOGY

De novotranscriptomic analyses for non-model organisms: an evaluation of methods across a multi-species data set

(2013) Sonal Singhal   Molecular Ecology Resources

Understanding the origin of species with genome-scale data: modelling gene flow

(2013) Vitor Sousa et al.   NATURE REVIEWS GENETICS

Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales

(2012) Ke Bi et al.   BMC GENOMICS

The Effects of Deleterious Mutations on Evolution at Linked Sites

(2012) Brian Charlesworth   GENETICS

Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex

(2012) Eric M. O'Neill et al.   MOLECULAR ECOLOGY

The simple fool's guide to population genomics via RNA-Seq: an introduction to high-throughput sequencing data analysis

(2012) Pierre De Wit et al.   Molecular Ecology Resources

Next-Generation Phylogeography: A Targeted Approach for Multilocus Sequencing of Non-Model Organisms

(2012) Jonathan B. Puritz et al.   PLoS One

The Development of Three Long Universal Nuclear Protein-Coding Locus Markers and Their Application to Osteichthyan Phylogenetics with Nested PCR

(2012) Xing-Xing Shen et al.   PLoS One

High-Throughput Identification of Informative Nuclear Loci for Shallow-Scale Phylogenetics and Phylogeography

(2012) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

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

Paired-end RAD-seq for de novo assembly and marker design without available reference

(2011) Eva-Maria Willing et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

A guided tour of large genome size in animals: what we know and where we are heading

(2011) France Dufresne et al.   CHROMOSOME RESEARCH

LTR Retrotransposons Contribute to Genomic Gigantism in Plethodontid Salamanders

(2011) Cheng Sun et al.   Genome Biology and Evolution

Next-generation hybridization and introgression

(2011) A D Twyford et al.   HEREDITY

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

Applications of next-generation sequencing to phylogeography and phylogenetics

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

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

Haplotype phasing: existing methods and new developments

(2011) Sharon R. Browning et al.   NATURE REVIEWS GENETICS

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

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

Exploiting Nucleotide Composition to Engineer Promoters

(2011) Manfred G. Grabherr et al.   PLoS One

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

Multiplex Manager 1.0: a cross-platform computer program that plans and optimizes multiplex PCR

(2009) Clare E. Holleley et al.   BIOTECHNIQUES

Genic regions of a large salamander genome contain long introns and novel genes

(2009) Jeramiah J Smith et al.   BMC GENOMICS

Divergence in the Face of Gene Flow: The Case of Two Newts (Amphibia: Salamandridae)

(2009) Krystyna Nadachowska et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogeography’s past, present, and future: 10 years after Avise, 2000

(2009) M.J. Hickerson et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Microdroplet-based PCR enrichment for large-scale targeted sequencing

(2009) Ryan Tewhey et al.   NATURE BIOTECHNOLOGY

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

BatchPrimer3: A high throughput web application for PCR and sequencing primer design

(2008) Frank M You et al.   BMC BIOINFORMATICS

Multilocus phylogeography and phylogenetics using sequence-based markers

(2008) Patrícia H. Brito et al.   GENETICA

Rapid development of multiple nuclear loci for phylogenetic analysis using genomic resources: An example from squamate reptiles

(2008) Ted M. Townsend et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

genepop’007: a complete re-implementation of the genepop software for Windows and Linux

(2007) FRANÇOIS ROUSSET   Molecular Ecology Resources