Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families

Distinct Viral Lineages from Fish and Amphibians Reveal the Complex Evolutionary History of Hepadnaviruses

(2016) Jennifer A. Dill et al.   JOURNAL OF VIROLOGY

Virological factors that increase the transmissibility of emerging human viruses

(2016) Jemma L. Geoghegan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pathogen population bottlenecks and adaptive landscapes: overcoming the barriers to disease emergence

(2016) Jemma L. Geoghegan et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Time scale evolution of avipoxviruses

(2015) Guillaume Le Loc’h et al.   INFECTION GENETICS AND EVOLUTION

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

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

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

(2015) Richard O. Prum et al.   NATURE

The evolution and emergence of hantaviruses

(2015) Edward C Holmes et al.   Current Opinion in Virology

Simulating and detecting autocorrelation of molecular evolutionary rates among lineages

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

Early Mesozoic Coexistence of Amniotes and Hepadnaviridae

(2014) Alexander Suh et al.   PLoS Genetics

Absence of Frequent Herpesvirus Transmission in a Nonhuman Primate Predator-Prey System in the Wild

(2013) S. Murthy et al.   JOURNAL OF VIROLOGY

Bats are a major natural reservoir for hepaciviruses and pegiviruses

(2013) P.-L. Quan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

(2012) S. Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Convergent Evolution of Escape from Hepaciviral Antagonism in Primates

(2012) Maulik R. Patel et al.   PLOS BIOLOGY

Reevaluating the Arthropod Tree of Life

(2011) Gonzalo Giribet et al.   Annual Review of Entomology

Paleozoic origin of insect large dsDNA viruses

(2011) J. Theze et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes

(2011) Maria Anisimova et al.   SYSTEMATIC BIOLOGY

Evaluating the evidence for virus/host co-evolution

(2011) Paul M Sharp et al.   Current Opinion in Virology

Jane: a new tool for the cophylogeny reconstruction problem

(2010) Chris Conow et al.   Algorithms for Molecular Biology

Viral Mutation Rates

(2010) R. Sanjuan et al.   JOURNAL OF VIROLOGY

Family level phylogenies reveal modes of macroevolution in RNA viruses

(2010) A. Kitchen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Island Biogeography Reveals the Deep History of SIV

(2010) M. Worobey et al.   SCIENCE

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

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

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

Cross-Species Virus Transmission and the Emergence of New Epidemic Diseases

(2008) C. R. Parrish et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS