The evolutionary history of vertebrate RNA viruses

Marine origin of retroviruses in the early Palaeozoic Era

(2017) Pakorn Aiewsakun et al.   Nature Communications

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

(2017) Jemma L. Geoghegan et al.   PLoS Pathogens

Ancient recombination events and the origins of hepatitis E virus

(2016) Andrew G. Kelly et al.   BMC EVOLUTIONARY BIOLOGY

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

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

Redefining the invertebrate RNA virosphere

(2016) Mang Shi et al.   NATURE

Divergent Viruses Discovered in Arthropods and Vertebrates Revise the Evolutionary History of the Flaviviridae and Related Viruses

(2015) Mang Shi et al.   JOURNAL OF VIROLOGY

Tree of Life Reveals Clock-Like Speciation and Diversification

(2015) S. Blair Hedges et al.   MOLECULAR BIOLOGY AND EVOLUTION

Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses

(2015) Ci-Xiu Li et al.   eLife

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

What is the time-scale of hantavirus evolution?

(2014) Yong-Zhen Zhang et al.   INFECTION GENETICS AND EVOLUTION

Characterization of a Novel Calicivirus Causing Systemic Infection in Atlantic Salmon (Salmo salar L.): Proposal for a New Genus of Caliciviridae

(2014) Aase B. Mikalsen et al.   PLoS One

A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors

(2014) X.-C. Qin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Cospeciation vs host-shift speciation: methods for testing, evidence from natural associations and relation to coevolution

(2013) D. M. de Vienne et al.   NEW PHYTOLOGIST

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Identification, Characterization, and In Vitro Culture of Highly Divergent Arenaviruses from Boa Constrictors and Annulated Tree Boas: Candidate Etiological Agents for Snake Inclusion Body Disease

(2012) M. D. Stenglein et al.   mBio

An Endogenous Foamy-like Viral Element in the Coelacanth Genome

(2012) Guan-Zhu Han et al.   PLoS Pathogens

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

Filoviruses are ancient and integrated into mammalian genomes

(2011) Derek J Taylor et al.   BMC EVOLUTIONARY BIOLOGY

Purifying Selection Can Obscure the Ancient Age of Viral Lineages

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

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

A novel member of the family Hepeviridae from cutthroat trout (Oncorhynchus clarkii)

(2011) William Batts et al.   VIRUS RESEARCH

Jane: a new tool for the cophylogeny reconstruction problem

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

Endogenous non-retroviral RNA virus elements in mammalian genomes

(2010) Masayuki Horie et al.   NATURE

Endogenous Viral Elements in Animal Genomes

(2010) Aris Katzourakis et al.   PLoS Genetics

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

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

Correlating viral phenotypes with phylogeny: Accounting for phylogenetic uncertainty

(2007) Joe Parker et al.   INFECTION GENETICS AND EVOLUTION