Improving the estimation of genetic distances from Next-Generation Sequencing data

ngsTools: methods for population genetics analyses from next-generation sequencing data

(2014) Matteo Fumagalli et al.   BIOINFORMATICS

Polymorphism in lake trout in Great Bear Lake: intra-lake morphological diversification at two spatial scales

(2014) Louise Chavarie et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears

(2014) Shiping Liu et al.   CELL

Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data

(2013) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation

(2013) Filipe G. Vieira et al.   GENOME RESEARCH

Linking Great Apes Genome Evolution across Time Scales Using Polymorphism-Aware Phylogenetic Models

(2013) Nicola De Maio et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bio++: Efficient Extensible Libraries and Tools for Computational Molecular Evolution

(2013) Laurent Guéguen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Unlocking the vault: next-generation museum population genomics

(2013) Ke Bi et al.   MOLECULAR ECOLOGY

Reference-Free Population Genomics from Next-Generation Transcriptome Data and the Vertebrate–Invertebrate Gap

(2013) Philippe Gayral et al.   PLoS Genetics

The Population Genomics of a Fast Evolver: High Levels of Diversity, Functional Constraint, and Molecular Adaptation in the Tunicate Ciona intestinalis

(2012) Georgia Tsagkogeorga et al.   Genome Biology and Evolution

A map of rice genome variation reveals the origin of cultivated rice

(2012) Xuehui Huang et al.   NATURE

SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data

(2012) Rasmus Nielsen et al.   PLoS One

A Fine-Scale Chimpanzee Genetic Map from Population Sequencing

(2012) A. Auton et al.   SCIENCE

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

(2011) H. Li   BIOINFORMATICS

Estimation of allele frequency and association mapping using next-generation sequencing data

(2011) Su Kim et al.   BMC BIOINFORMATICS

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

A Population Genetics-Phylogenetics Approach to Inferring Natural Selection in Coding Sequences

(2011) Daniel J. Wilson et al.   PLoS Genetics

MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus

(2010) Gregory Ewing et al.   BIOINFORMATICS

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

A Layered Grammar of Graphics

(2009) Hadley Wickham   JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Adaptations to Climate in Candidate Genes for Common Metabolic Disorders

(2008) Angela M. Hancock et al.   PLoS Genetics

Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation

(2008) J. Z. Li et al.   SCIENCE