Repeated divergent selection on pigmentation genes in a rapid finch radiation

Divergence and Functional Degradation of a Sex Chromosome-like Supergene

(2016) Elaina M. Tuttle et al.   CURRENT BIOLOGY

Plumage Genes and Little Else Distinguish the Genomes of Hybridizing Warblers

(2016) David P.L. Toews et al.   CURRENT BIOLOGY

Mutations in different pigmentation genes are associated with parallel melanism in island flycatchers

(2016) J. Albert C. Uy et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A beak size locus in Darwins finches facilitated character displacement during a drought

(2016) S. Lamichhaney et al.   SCIENCE

Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex

(2016) Nagarjun Vijay et al.   Nature Communications

Evolutionary Novelty in a Butterfly Wing Pattern through Enhancer Shuffling

(2016) Richard W. R. Wallbank et al.   PLOS BIOLOGY

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Distinguishing noise from signal in patterns of genomic divergence in a highly polymorphic avian radiation

(2015) Leonardo Campagna et al.   MOLECULAR ECOLOGY

Evolution of Darwin’s finches and their beaks revealed by genome sequencing

(2015) Sangeet Lamichhaney et al.   NATURE

Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax)

(2015) Sangeet Lamichhaney et al.   NATURE GENETICS

A supergene determines highly divergent male reproductive morphs in the ruff

(2015) Clemens Küpper et al.   NATURE GENETICS

PBHoney: identifying genomic variants via long-read discordance and interrupted mapping

(2014) Adam C English et al.   BMC BIOINFORMATICS

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Song-based species discrimination in a rapid Neotropical radiation of grassland seedeaters

(2014) Pilar Benites et al.   JOURNAL OF AVIAN BIOLOGY

Phylogenetics and diversification of tanagers (Passeriformes: Thraupidae), the largest radiation of Neotropical songbirds

(2014) Kevin J. Burns et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The genomic substrate for adaptive radiation in African cichlid fish

(2014) David Brawand et al.   NATURE

The genomic landscape underlying phenotypic integrity in the face of gene flow in crows

(2014) J. W. Poelstra et al.   SCIENCE

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Adaptive Evolution of Multiple Traits Through Multiple Mutations at a Single Gene

(2013) C. R. Linnen et al.   SCIENCE

Qualimap: evaluating next-generation sequencing alignment data

(2012) Fernando García-Alcalde et al.   BIOINFORMATICS

A high-performance computing toolset for relatedness and principal component analysis of SNP data

(2012) X. Zheng et al.   BIOINFORMATICS

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

(2012) M. Kearse et al.   BIOINFORMATICS

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter

(2012) M. Visser et al.   GENOME RESEARCH

Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

(2012) Kanchon K. Dasmahapatra et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

Diversification of complex butterfly wing patterns by repeated regulatory evolution of a Wnt ligand

(2012) A. Martin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Systematics of the Tawny-bellied Seedeater (Sporophila hypoxantha). I. Geographic Variation, Ecology, and Evolution of Vocalizations

(2011) Juan Ignacio Areta et al.   CONDOR

Rapid phenotypic evolution during incipient speciation in a continental avian radiation

(2011) L. Campagna et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genome-wide synteny through highly sensitive sequence alignment: Satsuma

(2010) M. G. Grabherr et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Landscape associations of globally threatened grassland birds in the Aguapey river Important Bird Area, Corrientes, Argentina

(2009) ADRIAN S. DI GIACOMO et al.   BIRD CONSERVATION INTERNATIONAL

MizBee: A Multiscale Synteny Browser

(2009) M. Meyer et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Genomic evidence for a large-Z effect

(2008) H. Ellegren   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Adaptation from standing genetic variation

(2007) R BARRETT et al.   TRENDS IN ECOLOGY & EVOLUTION