GLUE: a flexible software system for virus sequence data

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

Predicting the Effectiveness of Hepatitis C Virus Neutralizing Antibodies by Bioinformatic Analysis of Conserved Epitope Residues Using Public Sequence Data

(2018) Vanessa M. Cowton et al.   Frontiers in Immunology

GISAID: Global initiative on sharing all influenza data – from vision to reality

(2017) Yuelong Shu et al.   Eurosurveillance

EASL Recommendations on Treatment of Hepatitis C 2016

(2017)   JOURNAL OF HEPATOLOGY

Hepatitis C Virus Resistance to Direct-Acting Antiviral Drugs in Interferon-Free Regimens

(2016) Jean-Michel Pawlotsky   GASTROENTEROLOGY

The importance of resistance to direct antiviral drugs in HCV infection in clinical practice

(2016) Christoph Sarrazin   JOURNAL OF HEPATOLOGY

Expansion of the Gene Ontology knowledgebase and resources

(2016)   NUCLEIC ACIDS RESEARCH

Geno2pheno[HCV] – A Web-based Interpretation System to Support Hepatitis C Treatment Decisions in the Era of Direct-Acting Antiviral Agents

(2016) Prabhav Kalaghatgi et al.   PLoS One

nextflu: real-time tracking of seasonal influenza virus evolution in humans

(2015) Richard A. Neher et al.   BIOINFORMATICS

Hepatitis C virus drug resistance-associated substitutions: State of the art summary

(2015) Erik Lontok et al.   HEPATOLOGY

GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters

(2015) Itamar Sela et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2015) Karen Clark et al.   NUCLEIC ACIDS RESEARCH

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

The immune epitope database (IEDB) 3.0

(2014) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

The HIV Mutation Browser: A Resource for Human Immunodeficiency Virus Mutagenesis and Polymorphism Data

(2014) Norman E. Davey et al.   PLoS Computational Biology

Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: Updated criteria and genotype assignment web resource

(2013) Donald B. Smith et al.   HEPATOLOGY

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

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

Influenza Research Database: an integrated bioinformatics resource for influenza research and surveillance

(2012) R. Burke Squires et al.   Influenza and Other Respiratory Viruses

ViPR: an open bioinformatics database and analysis resource for virology research

(2011) Brett E. Pickett et al.   NUCLEIC ACIDS RESEARCH

Viral evolution in deep time: lentiviruses and mammals

(2011) Robert J. Gifford   TRENDS IN GENETICS

ViralZone: a knowledge resource to understand virus diversity

(2010) Chantal Hulo et al.   NUCLEIC ACIDS RESEARCH

The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance

(2009) R. J. Gifford et al.   BIOINFORMATICS

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

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences

(2009) L. C. J. Alcantara et al.   NUCLEIC ACIDS RESEARCH

Classification of hepatitis C virus and human immunodeficiency virus-1 sequences with the branching index

(2008) P. Hraber et al.   JOURNAL OF GENERAL VIROLOGY

The RNA Virus Database

(2008) Robert Belshaw et al.   NUCLEIC ACIDS RESEARCH