Ant phylogenomics reveals a natural selection hotspot preceding the origin of complex eusociality

Histone acetylation regulates the expression of genes involved in worker reproduction in the ant Temnothorax rugatulus

(2021) Marina Choppin et al.   BMC GENOMICS

The evolution of insect biodiversity

(2021) Erik Tihelka et al.   CURRENT BIOLOGY

CAFE 5 models variation in evolutionary rates among gene families

(2020) Fábio K Mendes et al.   BIOINFORMATICS

Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences

(2019) Arnaud Di Franco et al.   BMC EVOLUTIONARY BIOLOGY

Compositional heterogeneity and outgroup choice influence the internal phylogeny of the ants

(2019) Marek L. Borowiec et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Prevalence and Impact of Model Violations in Phylogenetic Analysis

(2019) Suha Naser-Khdour et al.   Genome Biology and Evolution

Evolutionary Models for the Diversification of Placental Mammals Across the KPg Boundary

(2019) Mark S. Springer et al.   Frontiers in Genetics

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

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

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

Macroecology and macroevolution of the latitudinal diversity gradient in ants

(2018) Evan P. Economo et al.   Nature Communications

Phenotypically distinct female castes in honey bees are defined by alternative chromatin states during larval development

(2018) Marek Wojciechowski et al.   GENOME RESEARCH

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter

(2017) Shaun D. Jackman et al.   GENOME RESEARCH

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation

(2017) Huai-Chun Wang et al.   SYSTEMATIC BIOLOGY

Analytical Biases Associated with GC-Content in Molecular Evolution

(2017) Jonathan Romiguier et al.   Frontiers in Genetics

Adaptive Radiation in Socially Advanced Stem-Group Ants from the Cretaceous

(2016) Phillip Barden et al.   CURRENT BIOLOGY

Defensive traits exhibit an evolutionary trade-off and drive diversification in ants

(2016) Benjamin D. Blanchard et al.   EVOLUTION

OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs

(2016) Evgeny M. Zdobnov et al.   NUCLEIC ACIDS RESEARCH

Tales of dracula ants: the evolutionary history of the ant subfamily Amblyoponinae (Hymenoptera: Formicidae)

(2016) PHILIP S. WARD et al.   SYSTEMATIC ENTOMOLOGY

PHYLUCE is a software package for the analysis of conserved genomic loci

(2015) Brant C. Faircloth   BIOINFORMATICS

Essential role for autophagy in life span extension

(2015) Frank Madeo et al.   JOURNAL OF CLINICAL INVESTIGATION

Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection

(2015) Martin D. Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

Epigenetic (re)programming of caste-specific behavior in the ant Camponotus floridanus

(2015) D. F. Simola et al.   SCIENCE

Epigenetic variation in the Egfr gene generates quantitative variation in a complex trait in ants

(2015) Sebastian Alvarado et al.   Nature Communications

The Phylogeny and Evolution of Ants

(2014) Philip S. Ward   Annual Review of Ecology Evolution and Systematics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum

(2014) John Gatesy et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Informed and automated k-mer size selection for genome assembly

(2013) R. Chikhi et al.   BIOINFORMATICS

TESTING THE MUSEUM VERSUS CRADLE TROPICAL BIOLOGICAL DIVERSITY HYPOTHESIS: PHYLOGENY, DIVERSIFICATION, AND ANCESTRAL BIOGEOGRAPHIC RANGE EVOLUTION OF THE ANTS

(2013) Corrie S. Moreau et al.   EVOLUTION

BLAST: a more efficient report with usability improvements

(2013) Grzegorz M. Boratyn et al.   NUCLEIC ACIDS RESEARCH

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Group Size and Its Effects on Collective Organization

(2011) Anna Dornhaus et al.   Annual Review of Entomology

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Histone deacetylase inhibitor activity in royal jelly might facilitate caste switching in bees

(2011) Astrid Spannhoff et al.   EMBO REPORTS

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

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

Improved Phylogenetic Analyses Corroborate a Plausible Position of Martialis heureka in the Ant Tree of Life

(2011) Patrick Kück et al.   PLoS One

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

(2011) Vincent Ranwez et al.   PLoS One

Statistical Properties of the Branch-Site Test of Positive Selection

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

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Newly discovered sister lineage sheds light on early ant evolution

(2008) C. Rabeling et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA