Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution

How do seemingly non-vagile clades accomplish trans-marine dispersal? Trait and dispersal evolution in the landfowl (Aves: Galliformes)

(2017) Peter A. Hosner et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ancestral range reconstruction of Galliformes: the effects of topology and taxon sampling

(2016) Ning Wang et al.   JOURNAL OF BIOGEOGRAPHY

PSMC analysis of effective population sizes in molecular ecology and its application to black-and-whiteFicedulaflycatchers

(2016) Krystyna Nadachowska-Brzyska et al.   MOLECULAR ECOLOGY

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Temporal Dynamics of Avian Populations during Pleistocene Revealed by Whole-Genome Sequences

(2015) Krystyna Nadachowska-Brzyska et al.   CURRENT BIOLOGY

Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes)

(2015) Peter A. Hosner et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic Analyses Reveal Potential Independent Adaptation to High Altitude in Tibetan Chickens

(2015) Ming-Shan Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Stable recombination hotspots in birds

(2015) S. Singhal et al.   SCIENCE

Systematic comparison of variant calling pipelines using gold standard personal exome variants

(2015) Sohyun Hwang et al.   Scientific Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution

(2014) Biao Wang et al.   BMC GENOMICS

Erasing Errors due to Alignment Ambiguity When Estimating Positive Selection

(2014) Benjamin Redelings   MOLECULAR BIOLOGY AND EVOLUTION

A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution

(2014) Takeshi Kawakami et al.   MOLECULAR ECOLOGY

A Draft De Novo Genome Assembly for the Northern Bobwhite (Colinus virginianus) Reveals Evidence for a Rapid Decline in Effective Population Size Beginning in the Late Pleistocene

(2014) Yvette A. Halley et al.   PLoS One

The Updated Phylogenies of the Phasianidae Based on Combined Data of Nuclear and Mitochondrial DNA

(2014) Yong-Yi Shen et al.   PLoS One

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

Species delimitation in the Chinese bamboo partridgeBambusicola thoracica(Phasianidae; Aves)

(2014) Chih-Ming Hung et al.   ZOOLOGICA SCRIPTA

Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix

(2014) Rebecca T. Kimball et al.   PeerJ

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

Next-generation sequencing reveals genomic features in the Japanese quail

(2013) Ryouka Kawahara-Miki et al.   GENOMICS

Mapping Genes to Chicken Microchromosome 16 and Discovery of Olfactory and Scavenger Receptor Genes Near the Major Histocompatibility Complex

(2013) Marcia M. Miller et al.   JOURNAL OF HEREDITY

Assessing Phylogenetic Relationships among Galliformes: A Multigene Phylogeny with Expanded Taxon Sampling in Phasianidae

(2013) Ning Wang et al.   PLoS One

Genome analysis reveals insights into physiology and longevity of the Brandt’s bat Myotis brandtii

(2013) Inge Seim et al.   Nature Communications

Using False Discovery Rates to Benchmark SNP-callers in next-generation sequencing projects

(2013) Rhys A. Farrer et al.   Scientific Reports

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

(2013) H Bradley Shaffer et al.   GENOME BIOLOGY

The yak genome and adaptation to life at high altitude

(2012) Qiang Qiu et al.   NATURE GENETICS

TreeFix: Statistically Informed Gene Tree Error Correction Using Species Trees

(2012) Yi-Chieh Wu et al.   SYSTEMATIC BIOLOGY

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

(2012) Ruibang Luo et al.   GigaScience

Consequences of Range Contractions and Range Shifts on Molecular Diversity

(2011) Miguel Arenas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Avian spurs

(2010) G. W. H. Davison   JOURNAL OF ZOOLOGY

Statistical Properties of the Branch-Site Test of Positive Selection

(2010) Z. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Effect of Insertions, Deletions, and Alignment Errors on the Branch-Site Test of Positive Selection

(2010) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogeography of Chinese bamboo partridge, Bambusicola thoracica thoracica (Aves: Galliformes) in south China: Inference from mitochondrial DNA control-region sequences

(2010) Zuhao Huang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Origin and Genetic Variation of Domestic Chickens with Special Reference to Junglefowls Gallus g. gallus and G. varius

(2010) Hiromi Sawai et al.   PLoS One

Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis

(2010) Rami A. Dalloul et al.   PLOS BIOLOGY

Molecular evolution of genes in avian genomes

(2010) Kiwoong Nam et al.   GENOME BIOLOGY

ABySS: A parallel assembler for short read sequence data

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

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH