A Roadmap for Genome-Based Phage Taxonomy

ICTV Virus Taxonomy Profile: Herelleviridae

(2020) Jakub Barylski et al.   JOURNAL OF GENERAL VIROLOGY

Global Organization and Proposed Megataxonomy of the Virus World

(2020) Eugene V. Koonin et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Clades of huge phages from across Earth’s ecosystems

(2020) Basem Al-Shayeb et al.   NATURE

Expansion of known ssRNA phage genomes: From tens to over a thousand

(2020) J. Callanan et al.   Science Advances

Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

(2020) Evelien M. Adriaenssens et al.   ARCHIVES OF VIROLOGY

The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks

(2020)   Nature Microbiology

The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut

(2020) Ann C. Gregory et al.   Cell Host & Microbe

ICTV Virus Taxonomy Profile: Finnlakeviridae

(2020) Sari Mäntynen et al.   JOURNAL OF GENERAL VIROLOGY

From Orphan Phage to a Proposed New Family–The Diversity of N4-Like Viruses

(2020) Johannes Wittmann et al.   Antibiotics-Basel

Megaphages infect Prevotella and variants are widespread in gut microbiomes

(2019) Audra E. Devoto et al.   Nature Microbiology

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

(2019) Ho Bin Jang et al.   NATURE BIOTECHNOLOGY

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages

(2019) Jakub Barylski et al.   SYSTEMATIC BIOLOGY

Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales

(2019) Soo Jen Low et al.   Nature Microbiology

Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes

(2019) Simon Roux et al.   Nature Microbiology

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

(2019) Robert A. Edwards et al.   Nature Microbiology

PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria

(2019) Sion C Bayliss et al.   GigaScience

Defining a Core Genome for the Herpesvirales and Exploring their Evolutionary Relationship with the Caudovirales

(2019) Juan S. Andrade-Martínez et al.   Scientific Reports

Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

(2018) Evelien M. Adriaenssens et al.   ARCHIVES OF VIROLOGY

Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: steps towards a unified taxonomy

(2018) Pakorn Aiewsakun et al.   JOURNAL OF GENERAL VIROLOGY

The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

(2018) Pakorn Aiewsakun et al.   Microbiome

A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria

(2018) Kathryn M. Kauffman et al.   NATURE

Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut

(2018) Emma Guerin et al.   Cell Host & Microbe

Minimum Information about an Uncultivated Virus Genome (MIUViG)

(2018) Simon Roux et al.   NATURE BIOTECHNOLOGY

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Virus found in a boreal lake links ssDNA and dsDNA viruses

(2017) Elina Laanto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria

(2017) Benjamin Bolduc et al.   PeerJ

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

(2016) Mart Krupovic et al.   ARCHIVES OF VIROLOGY

Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer

(2016) Ann C. Gregory et al.   BMC GENOMICS

The Double-Stranded DNA Virosphere as a Modular Hierarchical Network of Gene Sharing

(2016) Jaime Iranzo et al.   mBio

Hyperexpansion of RNA Bacteriophage Diversity

(2016) Siddharth R. Krishnamurthy et al.   PLOS BIOLOGY

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

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

(2015) Evelien M. Adriaenssens et al.   VIROLOGY

Diversity and comparative genomics of Microviridae in Sphagnum- dominated peatlands

(2015) Achim Quaiser et al.   Frontiers in Microbiology

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

(2014) Bas E. Dutilh et al.   Nature Communications

GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis

(2013) Bruno Contreras-Moreira et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Evolution and Diversity of the Microviridae Viral Family through a Collection of 81 New Complete Genomes Assembled from Virome Reads

(2012) Simon Roux et al.   PLoS One

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

InterPro in 2011: new developments in the family and domain prediction database

(2011) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Microviridae Goes Temperate: Microvirus-Related Proviruses Reside in the Genomes of Bacteroidetes

(2011) Mart Krupovic et al.   PLoS One

Classification of Myoviridae bacteriophages using protein sequence similarity

(2009) Rob Lavigne et al.   BMC 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

CDD: specific functional annotation with the Conserved Domain Database

(2008) A. Marchler-Bauer 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