RELAX: Detecting Relaxed Selection in a Phylogenetic Framework

Massive Losses of Taste Receptor Genes in Toothed and Baleen Whales

(2014) Ping Feng et al.   Genome Biology and Evolution

Relaxed functional constraints on triplicate α-globin gene in the bank vole suggest a different evolutionary history from other rodents

(2014) S Marková et al.   HEREDITY

On the Validity of Evolutionary Models with Site-Specific Parameters

(2014) Konrad Scheffler et al.   PLoS One

On the Immortality of Television Sets: "Function" in the Human Genome According to the Evolution-Free Gospel of ENCODE

(2013) D. Graur et al.   Genome Biology and Evolution

Nocturnal Light Environments Influence Color Vision and Signatures of Selection on the OPN1SW Opsin Gene in Nocturnal Lemurs

(2013) Carrie C. Veilleux et al.   MOLECULAR BIOLOGY AND EVOLUTION

Disproportional Plastome-Wide Increase of Substitution Rates and Relaxed Purifying Selection in Genes of Carnivorous Lentibulariaceae

(2013) Susann Wicke et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comprehensive analysis of endogenous bornavirus-like elements in eukaryote genomes

(2013) M. Horie et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Population-genomic insights into the evolutionary origin and fate of obligately asexual Daphnia pulex

(2013) A. E. Tucker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of high duty cycle echolocation in bats

(2012) M. B. Fenton et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

GLADX: An Automated Approach to Analyze the Lineage-Specific Loss and Pseudogenization of Genes

(2012) Jacques Dainat et al.   PLoS One

Detecting Individual Sites Subject to Episodic Diversifying Selection

(2012) Ben Murrell et al.   PLoS Genetics

Multiple origins of endosymbiosis within the Enterobacteriaceae (γ-Proteobacteria): convergence of complex phylogenetic approaches

(2011) Filip Husník et al.   BMC BIOLOGY

A Random Effects Branch-Site Model for Detecting Episodic Diversifying Selection

(2011) Sergei L. Kosakovsky Pond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Purifying Selection Can Obscure the Ancient Age of Viral Lineages

(2011) Joel O. Wertheim et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reduced Selective Constraint in Endosymbionts: Elevation in Radical Amino Acid Replacements Occurs Genome-Wide

(2011) Jennifer J. Wernegreen   PLoS One

Relaxed selection is a precursor to the evolution of phenotypic plasticity

(2011) B. G. Hunt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology

(2010) W. Delport et al.   BIOINFORMATICS

Endogenous non-retroviral RNA virus elements in mammalian genomes

(2010) Masayuki Horie et al.   NATURE

Correcting the Bias of Empirical Frequency Parameter Estimators in Codon Models

(2010) Sergei Kosakovsky Pond et al.   PLoS One

Sources of variation in dietary requirements in an obligate nutritional symbiosis

(2010) K. J. Vogel et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Unexpected Inheritance: Multiple Integrations of Ancient Bornavirus and Ebolavirus/Marburgvirus Sequences in Vertebrate Genomes

(2010) Vladimir A. Belyi et al.   PLoS Pathogens

Toward a population genetic framework of developmental evolution: the costs, limits, and consequences of phenotypic plasticity

(2009) Emilie C. Snell-Rood et al.   BIOESSAYS

Effects of facultative symbionts and heat stress on the metabolome of pea aphids

(2009) Gaelen Burke et al.   ISME Journal

Relaxed Selection and the Evolution of RNA Virus Mucin-Like Pathogenicity Factors

(2009) J. O. Wertheim et al.   JOURNAL OF VIROLOGY

Evolutionary Fingerprinting of Genes

(2009) S. L. Kosakovsky Pond et al.   MOLECULAR BIOLOGY AND EVOLUTION

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolutionary conundrum of pathogen mimicry

(2009) Nels C. Elde et al.   NATURE REVIEWS MICROBIOLOGY

Rhodopsin Molecular Evolution in Mammals Inhabiting Low Light Environments

(2009) Huabin Zhao et al.   PLoS One

The evolution of color vision in nocturnal mammals

(2009) H. Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors

(2009) P. H. Degnan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Convergent evolution of metabolic roles in bacterial co-symbionts of insects

(2009) J. P. McCutcheon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacteriophages Encode Factors Required for Protection in a Symbiotic Mutualism

(2009) K. M. Oliver et al.   SCIENCE

Relaxed selection in the wild

(2009) David C. Lahti et al.   TRENDS IN ECOLOGY & EVOLUTION

The reality and importance of founder speciation in evolution

(2008) Alan R. Templeton   BIOESSAYS

Models of coding sequence evolution

(2008) W. Delport et al.   BRIEFINGS IN BIOINFORMATICS

Investigating Protein-Coding Sequence Evolution with Probabilistic Codon Substitution Models

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

The visual system in subterranean African mole-rats (Rodentia, Bathyergidae): Retina, subcortical visual nuclei and primary visual cortex

(2007) Pavel Němec et al.   BRAIN RESEARCH BULLETIN