Substitution Model Adequacy and Assessing the Reliability of Estimates of Virus Evolutionary Rates and Time Scales

Declining transition/transversion ratios through time reveal limitations to the accuracy of nucleotide substitution models

(2015) Sebastián Duchêne et al.   BMC EVOLUTIONARY BIOLOGY

Emergence and potential for spread of Chikungunya virus in Brazil

(2015) Marcio Roberto Teixeira Nunes et al.   BMC Medicine

Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations

(2015) David A. Duchêne et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Relationship between dN/dS and Scaled Selection Coefficients

(2015) Stephanie J. Spielman et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Performance of the Date-Randomization Test in Phylogenetic Analyses of Time-Structured Virus Data

(2015) Sebastián Duchêne et al.   MOLECULAR BIOLOGY AND EVOLUTION

Can We Identify Genes with Increased Phylogenetic Reliability?

(2015) Vinson P. Doyle et al.   SYSTEMATIC BIOLOGY

New Insights into Flavivirus Evolution, Taxonomy and Biogeographic History, Extended by Analysis of Canonical and Alternative Coding Sequences

(2015) Gregory Moureau et al.   PLoS One

Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies

(2015) Stephanie J. Spielman et al.   PLoS One

Dating the origin of the genus Flavivirus in the light of Beringian biogeography

(2014) J. H.- O. Pettersson et al.   JOURNAL OF GENERAL VIROLOGY

Molecular-clock methods for estimating evolutionary rates and timescales

(2014) Simon Y. W. Ho et al.   MOLECULAR ECOLOGY

Tree imbalance causes a bias in phylogenetic estimation of evolutionary timescales using heterochronous sequences

(2014) David Duchêne et al.   Molecular Ecology Resources

Simulating and detecting autocorrelation of molecular evolutionary rates among lineages

(2014) Simon Y. W. Ho et al.   Molecular Ecology Resources

Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates

(2014) S. Duchene et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Predictive Approaches to Assessing the Fit of Evolutionary Models

(2014) Jeremy M. Brown   SYSTEMATIC BIOLOGY

Detection of Implausible Phylogenetic Inferences Using Posterior Predictive Assessment of Model Fit

(2014) Jeremy M. Brown   SYSTEMATIC BIOLOGY

Air Travel Is Associated with Intracontinental Spread of Dengue Virus Serotypes 1–3 in Brazil

(2014) Marcio R. T. Nunes et al.   PLoS Neglected Tropical Diseases

A Case for the Ancient Origin of Coronaviruses

(2013) J. O. Wertheim et al.   JOURNAL OF VIROLOGY

Viral Phylodynamics

(2013) Erik M. Volz et al.   PLoS Computational Biology

ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R

(2012) Andrei-Alin Popescu et al.   BIOINFORMATICS

Philosophy and the practice of Bayesian statistics

(2012) Andrew Gelman et al.   BRITISH JOURNAL OF MATHEMATICAL & STATISTICAL PSYCHOLOGY

Evolutionary and ecological factors underlying the tempo and distribution of yellow fever virus activity

(2012) Christine V.F. Carrington et al.   INFECTION GENETICS AND EVOLUTION

Revisiting the Clinal Concept of Evolution and Dispersal for the Tick-Borne Flaviviruses by Using Phylogenetic and Biogeographic Analyses

(2012) D. M. Heinze et al.   JOURNAL OF VIROLOGY

Discovery of Seven Novel Mammalian and Avian Coronaviruses in the Genus Deltacoronavirus Supports Bat Coronaviruses as the Gene Source of Alphacoronavirus and Betacoronavirus and Avian Coronaviruses as the Gene Source of Gammacoronavirus and Deltacoronavirus

(2012) P. C. Y. Woo et al.   JOURNAL OF VIROLOGY

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

From Molecular Genetics to Phylodynamics: Evolutionary Relevance of Mutation Rates Across Viruses

(2012) Rafael Sanjuán   PLoS Pathogens

Phylogenetic and epidemic modeling of rapidly evolving infectious diseases

(2011) Denise Kühnert et al.   INFECTION GENETICS AND EVOLUTION

Purifying Selection Can Obscure the Ancient Age of Viral Lineages

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

Viral mutation and substitution: units and levels

(2011) Robert Belshaw et al.   Current Opinion in Virology

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Genome-Scale Phylogenetic Analyses of Chikungunya Virus Reveal Independent Emergences of Recent Epidemics and Various Evolutionary Rates

(2010) S. M. Volk et al.   JOURNAL OF VIROLOGY

Assessment of Substitution Model Adequacy Using Frequentist and Bayesian Methods

(2010) Jennifer Ripplinger et al.   MOLECULAR BIOLOGY AND EVOLUTION

Using Time-Structured Data to Estimate Evolutionary Rates of Double-Stranded DNA Viruses

(2010) C. Firth et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection

(2010) Wangang Xie et al.   SYSTEMATIC BIOLOGY

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Phylodynamics of Infectious Disease Epidemics

(2009) Erik M. Volz et al.   GENETICS

Yellow Fever Virus Exhibits Slower Evolutionary Dynamics than Dengue Virus

(2009) A. A. Sall et al.   JOURNAL OF VIROLOGY

Branch-length estimation bias misleads molecular dating for a vertebrate mitochondrial phylogeny

(2008) Matthew J. Phillips   GENE

Calibration of Multiple Poliovirus Molecular Clocks Covering an Extended Evolutionary Range

(2008) J. Jorba et al.   JOURNAL OF VIROLOGY

Hantavirus Evolution in Relation to Its Rodent and Insectivore Hosts: No Evidence for Codivergence

(2008) C. Ramsden et al.   MOLECULAR BIOLOGY AND EVOLUTION

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian analysis of amino acid substitution models

(2008) J. P Huelsenbeck et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES