The Genome of the Endangered Dryas Monkey Provides New Insights into the Evolutionary History of the Vervets

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Natural selection interacts with recombination to shape the evolution of hybrid genomes

(2018) Molly Schumer et al.   SCIENCE

Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case

(2018) Mario Dos Reis et al.   SYSTEMATIC BIOLOGY

Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas

(2018) Tom van der Valk et al.   CURRENT BIOLOGY

Selective single molecule sequencing and assembly of a human Y chromosome of African origin

(2018) Lukas F. K. Kuderna et al.   Nature Communications

Direct estimate of the spontaneous germ line mutation rate in African green monkeys

(2017) Susanne P. Pfeifer   EVOLUTION

Exploring Evolutionary Relationships Across the Genome Using Topology Weighting

(2017) Simon H. Martin et al.   GENETICS

Introgression Makes Waves in Inferred Histories of Effective Population Size

(2017) John Hawks   HUMAN BIOLOGY

Ancient hybridization and strong adaptation to viruses across African vervet monkey populations

(2017) Hannes Svardal et al.   NATURE GENETICS

Y and W Chromosome Assemblies: Approaches and Discoveries

(2017) Marta Tomaszkiewicz et al.   TRENDS IN GENETICS

Exploring Evolutionary Relationships Across the Genome Using Topology Weighting

(2017) Simon H. Martin et al.   GENETICS

The population genomics of rhesus macaques ( Macaca mulatta ) based on whole-genome sequences

(2016) Cheng Xue et al.   GENOME RESEARCH

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

(2016) Erfan Sayyari et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Ancient gene flow from early modern humans into Eastern Neanderthals

(2016) Martin Kuhlwilm et al.   NATURE

NOVOPlasty:de novoassembly of organelle genomes from whole genome data

(2016) Nicolas Dierckxsens et al.   NUCLEIC ACIDS RESEARCH

Inferring species divergence times using pairwise sequential Markovian coalescent modelling and low-coverage genomic data

(2016) James A. Cahill et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Chimpanzee genomic diversity reveals ancient admixture with bonobos

(2016) M. de Manuel et al.   SCIENCE

The genome of the vervet (Chlorocebus aethiops sabaeus)

(2015) Wesley C. Warren et al.   GENOME RESEARCH

SEPT12 orchestrates the formation of mammalian sperm annulus by organizing core octameric complexes with other SEPT proteins

(2015) Y.-C. Kuo et al.   JOURNAL OF CELL SCIENCE

Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding

(2015) Y. Xue et al.   SCIENCE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

The Lengths of Admixture Tracts

(2014) M. Liang et al.   GENETICS

Neurocysticercosis: the effectiveness of the cysticidal treatment could be influenced by the host immunity

(2014) Graciela Cárdenas et al.   MEDICAL MICROBIOLOGY AND IMMUNOLOGY

Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci

(2014) Simon H. Martin et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genomic landscape of Neanderthal ancestry in present-day humans

(2014) Sriram Sankararaman et al.   NATURE

Distinct and Diverse: Range-Wide Phylogeography Reveals Ancient Lineages and High Genetic Variation in the Endangered Okapi (Okapia johnstoni)

(2014) David W. G. Stanton et al.   PLoS One

Haplotype Estimation Using Sequencing Reads

(2013) Olivier Delaneau et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Mitochondrial Diversity and Distribution of African Green Monkeys (ChlorocebusGray, 1870)

(2013) TANJA HAUS et al.   AMERICAN JOURNAL OF PRIMATOLOGY

Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data

(2013) Matteo Fumagalli et al.   GENETICS

Assessing the Effect of Sequencing Depth and Sample Size in Population Genetics Inferences

(2013) Matteo Fumagalli   PLoS One

Next-Generation Museomics Disentangles One of the Largest Primate Radiations

(2013) Katerina Guschanski et al.   SYSTEMATIC BIOLOGY

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

(2012) Joseph K. Pickrell et al.   PLoS Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Approximate Likelihood Calculation on a Phylogeny for Bayesian Estimation of Divergence Times

(2011) M. d. Reis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

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

(2011) Mark A DePristo et al.   NATURE GENETICS

The Ins and Outs of HIV-1 Tat

(2011) Solène Debaisieux et al.   TRAFFIC

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

PHAST and RPHAST: phylogenetic analysis with space/time models

(2010) M. J. Hubisz et al.   BRIEFINGS IN BIOINFORMATICS

Population differentiation as a test for selective sweeps

(2010) H. Chen et al.   GENOME RESEARCH

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

(2010) A. McKenna et al.   GENOME RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

AEBP2 as a potential targeting protein for Polycomb Repression Complex PRC2

(2009) Hana Kim et al.   NUCLEIC ACIDS RESEARCH

Subdivision in an Ancestral Species Creates Asymmetry in Gene Trees

(2008) M. Slatkin et al.   MOLECULAR BIOLOGY AND EVOLUTION

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH