The draft genome of the pest tephritid fruit fly Bactrocera tryoni: resources for the genomic analysis of hybridising species

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

DSK: k-mer counting with very low memory usage

(2013) G. Rizk et al.   BIOINFORMATICS

Divergent Selection Drives Genetic Differentiation in an R2R3-MYB Transcription Factor That Contributes to Incipient Speciation in Mimulus aurantiacus

(2013) Matthew A. Streisfeld et al.   PLoS Genetics

Genome sequencing reveals complex speciation in the Drosophila simulans clade

(2012) D. Garrigan et al.   GENOME RESEARCH

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Quake: quality-aware detection and correction of sequencing errors

(2012) David R Kelley et al.   GENOME BIOLOGY

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Characterization of the Conus bullatus genome and its venom-duct transcriptome

(2011) Hao Hu et al.   BMC GENOMICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The genes underlying the process of speciation

(2011) Patrik Nosil et al.   TRENDS IN ECOLOGY & EVOLUTION

The draft genome of the carcinogenic human liver fluke Clonorchis sinensis

(2011) Xiaoyun Wang et al.   GENOME BIOLOGY

Global sequence characterization of rice centromeric satellite based on oligomer frequency analysis in large-scale sequencing data

(2010) J. Macas et al.   BIOINFORMATICS

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Fusion–fission experiments in Aphidius: evolutionary split without isolation in response to environmental bimodality

(2010) I Emelianov et al.   HEREDITY

Transcriptome-wide signature of hybrid breakdown associated with intrinsic reproductive isolation in lake whitefish species pairs (Coregonus spp. Salmonidae)

(2010) S Renaut et al.   HEREDITY

Interspecific Hybridization as a Source of Novel Genetic Markers for the Sterile Insect Technique in Bactrocera tryoni (Diptera: Tephritidae)

(2010) D. C. A. Shearman et al.   JOURNAL OF ECONOMIC ENTOMOLOGY

Domestication of olive fly through a multi-regional host shift to cultivated olives: Comparative dating using complete mitochondrial genomes

(2010) F. Nardi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A golden age for evolutionary genetics? Genomic studies of adaptation in natural populations

(2010) Nicola J. Nadeau et al.   TRENDS IN GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Big Genomes Facilitate the Comparative Identification of Regulatory Elements

(2009) Brant K. Peterson et al.   PLoS One

Natural selection in action during speciation

(2009) S. Via   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Genomics of Speciation in Drosophila: Diversity, Divergence, and Introgression Estimated Using Low-Coverage Genome Sequencing

(2009) Rob J. Kulathinal et al.   PLoS Genetics

Satellite DNA in insects: a review

(2008) T Palomeque et al.   HEREDITY