How to Name and Classify Your Phage: An Informal Guide

Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee

(2016) Evelien M. Adriaenssens et al.   ARCHIVES OF VIROLOGY

Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee

(2016) Mart Krupovic et al.   ARCHIVES OF VIROLOGY

Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation

(2016) Ana Laura Grazziotin et al.   NUCLEIC ACIDS RESEARCH

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Putative type 1 thymidylate synthase and dihydrofolate reductase as signature genes of a novel bastille-like group of phages in the subfamily Spounavirinae

(2015) Paul Tetteh Asare et al.   BMC GENOMICS

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Integration of genomic and proteomic analyses in the classification of the Siphoviridae family

(2015) Evelien M. Adriaenssens et al.   VIROLOGY

Genomic characteristics and environmental distributions of the uncultivated Far-T4 phages

(2015) Simon Roux et al.   Frontiers in Microbiology

Improvements to pairwise sequence comparison (PASC): a genome-based web tool for virus classification

(2014) Yiming Bao et al.   ARCHIVES OF VIROLOGY

NCBI Viral Genomes Resource

(2014) J. Rodney Brister et al.   NUCLEIC ACIDS RESEARCH

Understanding the enormous diversity of bacteriophages: The tailed phages that infect the bacterial family Enterobacteriaceae

(2014) Julianne H. Grose et al.   VIROLOGY

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gegenees: Fragmented Alignment of Multiple Genomes for Determining Phylogenomic Distances and Genetic Signatures Unique for Specified Target Groups

(2012) Joakim Ågren et al.   PLoS One

Easyfig: a genome comparison visualizer

(2011) M. J. Sullivan et al.   BIOINFORMATICS

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

The International Nucleotide Sequence Database Collaboration

(2011) I. Karsch-Mizrachi et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Genomes of the T4-related bacteriophages as windows on microbial genome evolution

(2010) Vasiliy M Petrov et al.   Virology Journal

Classification of Myoviridae bacteriophages using protein sequence similarity

(2009) Rob Lavigne et al.   BMC MICROBIOLOGY

Position paper: The creation of a rational scheme for the nomenclature of viruses ofBacteriaandArchaea

(2009) Andrew M. Kropinski et al.   ENVIRONMENTAL MICROBIOLOGY

Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes

(2008) G. Lima-Mendez et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogeny.fr: robust phylogenetic analysis for the non-specialist

(2008) A. Dereeper et al.   NUCLEIC ACIDS RESEARCH

NCBI BLAST: a better web interface

(2008) M. Johnson et al.   NUCLEIC ACIDS RESEARCH

Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools

(2008) Rob Lavigne et al.   RESEARCH IN MICROBIOLOGY