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

https://doi.org/10.1093/sysbio/syz036
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages 1 1Edited by M. Gottesman
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50 years of the International Committee on Taxonomy of Viruses: progress and prospects
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Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee
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Virus classification – where do you draw the line?
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Comparison of phylogenetic trees
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Understanding the enormous diversity of bacteriophages: The tailed phages that infect the bacterial family Enterobacteriaceae
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A structured annotation frame for the transposable phages: A new proposed family “Saltoviridae” within the Caudovirales
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The rapid generation of mutation data matrices from protein sequences
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CLANS: a Java application for visualizing protein families based on pairwise similarity
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Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation
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Clustal W and Clustal X version 2.0
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CD-HIT: accelerated for clustering the next-generation sequencing data
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Prokka: rapid prokaryotic genome annotation
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Roary: rapid large-scale prokaryote pan genome analysis
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ViPTree: the viral proteomic tree server
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VICTOR: genome-based phylogeny and classification of prokaryotic viruses
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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
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FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program: Table 1.
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UFBoot2: Improving the Ultrafast Bootstrap Approximation
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An efficient algorithm for large-scale detection of protein families
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The HHpred interactive server for protein homology detection and structure prediction
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HMMER web server: interactive sequence similarity searching
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NCBI Viral Genomes Resource
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Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
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Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation
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A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach
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BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data
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Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks
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Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices
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Journal of General Virology – Introduction to ‘ICTV Virus Taxonomy Profiles’
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Notices
inferredcites →https://doi.org/10.1111/j.1574-6968.2007.00996.xopenalex-snapshot
Isolation and characterization of a novelEnterococcus faecalisbacteriophage φEF24C as a therapeutic candidate
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In Silico and In Vivo Evaluation of Bacteriophage φEF24C, a Candidate for Treatment of Enterococcus faecalis Infections
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GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis
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Effects of Actin-Like Proteins Encoded by Two Bacillus pumilus Phages on Unstable Lysogeny, Revealed by Genomic Analysis
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Complete Genome Sequence of Bacillus megaterium Myophage Mater
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Complete Genome Sequence of Bacillus megaterium Myophage Moonbeam
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The Phage Proteomic Tree: a Genome-Based Taxonomy for Phage
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Towards a Genome-Based Taxonomy for Prokaryotes
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The Double-Stranded DNA Virosphere as a Modular Hierarchical Network of Gene Sharing
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Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere
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Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean
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BLAST+: architecture and applications
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Prodigal: prokaryotic gene recognition and translation initiation site identification
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Genomic fluidity: an integrative view of gene diversity within microbial populations
inferredcites →https://doi.org/10.1186/1471-2164-16-s10-s1openalex-snapshot
Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer
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Classification of Myoviridae bacteriophages using protein sequence similarity
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The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification
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Expanding the Marine Virosphere Using Metagenomics
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Molecular Taxonomy of Phytopathogenic Fungi: A Case Study in Peronospora
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The Secret Life of the Anthrax Agent Bacillus anthracis: Bacteriophage-Mediated Ecological Adaptations
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FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
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RAxML and FastTree: Comparing Two Methods for Large-Scale Maximum Likelihood Phylogeny Estimation
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Gegenees: Fragmented Alignment of Multiple Genomes for Determining Phylogenomic Distances and Genetic Signatures Unique for Specified Target Groups
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The Discovery of phiAGATE, A Novel Phage Infecting Bacillus pumilus, Leads to New Insights into the Phylogeny of the Subfamily Spounavirinae
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Group I Introns in Staphylococcus Bacteriophages
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R: A Language and Environment for Statistical Computing
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vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Computational Tools for the Analysis of Uncultivated Phage Genomes
inferred← citeshttps://doi.org/10.1128/mmbr.00061-19openalex-snapshot
Global Organization and Proposed Megataxonomy of the Virus World
inferred← citeshttps://doi.org/10.1128/mra.00544-24openalex-snapshot
Complete genome sequences of Klebsiella pneumoniae bacteriophages YMR1 and YMR2 isolated from sewage
inferred← citeshttps://doi.org/10.1128/msphere.00297-22openalex-snapshot
Phage-Encoded Sigma Factors Alter Bacterial Dormancy
inferred← citeshttps://doi.org/10.1128/msystems.00994-22openalex-snapshot
Viral Community Structure and Potential Functions in the Dried-Out Aral Sea Basin Change along a Desiccation Gradient
inferred← citeshttps://doi.org/10.1128/spectrum.00998-24openalex-snapshot
Dysbiosis of gut microbiota in COVID-19 is associated with intestinal DNA phage dynamics of lysogenic and lytic infection
inferred← citeshttps://doi.org/10.1128/spectrum.01301-24openalex-snapshot
Physicochemical, genomic, and phenotypic characterization of Escherichia phage BME3
inferred← citeshttps://doi.org/10.1146/annurev-virology-100424-103106openalex-snapshot
What's in a Name? Upgrading Virus Species Nomenclature
inferred← citeshttps://doi.org/10.11606/d.95.2019.tde-24042019-115926openalex-snapshot
Construção e aplicação de HMMs de perfil para a detecção e classificação de vírus
inferred← citeshttps://doi.org/10.1186/s12864-020-6765-zopenalex-snapshot
Comparative genomic analysis of 142 bacteriophages infecting Salmonella enterica subsp. enterica
inferred← citeshttps://doi.org/10.1186/s12864-022-09055-wopenalex-snapshot
Genomic diversity and comprehensive taxonomical classification of 61 Bacillus subtilis group member infecting bacteriophages, and the identification of ortholog taxonomic signature genes
inferred← citeshttps://doi.org/10.1186/s12879-024-09152-zopenalex-snapshot
Isolation and characterization of lytic bacteriophages from various sources in Addis Ababa against antimicrobial-resistant diarrheagenic Escherichia coli strains and evaluation of their therapeutic potential
inferred← citeshttps://doi.org/10.1186/s40168-021-01017-wopenalex-snapshot
Thousands of previously unknown phages discovered in whole-community human gut metagenomes
inferred← citeshttps://doi.org/10.1186/s43088-021-00141-8openalex-snapshot
Phage therapy as a revolutionary medicine against Gram-positive bacterial infections
inferred← citeshttps://doi.org/10.1371/journal.pbio.3001442openalex-snapshot
Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes
inferred← citeshttps://doi.org/10.1371/journal.pbio.3001922openalex-snapshot
Four principles to establish a universal virus taxonomy
inferred← citeshttps://doi.org/10.14309/ctg.0000000000000659openalex-snapshot
Proton Pump Inhibitor Use and Complications of Cirrhosis Are Linked With Distinct Gut Microbial Bacteriophage and Eukaryotic Viral-Like Particle Signatures in Cirrhosis
inferred← citeshttps://doi.org/10.18524/2307-4663.2022.1(54).219213openalex-snapshot
PHAGES OF BACTERIА OF THE GENUS BACILLUS ISOLATED FROM THE AQUATIC ENVIRONMENT
inferred← citeshttps://doi.org/10.21203/rs.3.rs-4823775/v1openalex-snapshot
Alterations of the gut virome in patients with Parkinson's disease
inferred← citeshttps://doi.org/10.3136/nskkk.67.352openalex-snapshot
Development of a Novel Food Antimicrobial Technology: Application of Bacteriophages
inferred← citeshttps://doi.org/10.3389/fendo.2019.00784openalex-snapshot
Gut Bacteriophage: Current Understanding and Challenges
inferred← citeshttps://doi.org/10.3389/fmicb.2018.03227openalex-snapshot
The Ability of Lytic Staphylococcal Podovirus vB_SauP_phiAGO1.3 to Coexist in Equilibrium With Its Host Facilitates the Selection of Host Mutants of Attenuated Virulence but Does Not Preclude the Phage Antistaphylococcal Activity in a Nematode Infection Model
inferred← citeshttps://doi.org/10.3389/fmicb.2020.00450openalex-snapshot
Rumen Virus Populations: Technological Advances Enhancing Current Understanding
inferred← citeshttps://doi.org/10.3389/fmicb.2021.625599openalex-snapshot
Cellular and Genomic Properties of Haloferax gibbonsii LR2-5, the Host of Euryarchaeal Virus HFTV1
inferred← citeshttps://doi.org/10.3389/fmicb.2021.660351openalex-snapshot
A Novel Jumbo Phage PhiMa05 Inhibits Harmful Microcystis sp.
inferred← citeshttps://doi.org/10.3389/fmicb.2023.1120147openalex-snapshot
Genome, biology and stability of the Thurquoise phage – A new virus from the Bastillevirinae subfamily
inferred← citeshttps://doi.org/10.3389/fmicb.2024.1400700openalex-snapshot
Characterization and genomic analysis of a lytic Stenotrophomonas maltophilia short-tailed phage A1432 revealed a new genus of the family Mesyanzhinovviridae
inferred← citeshttps://doi.org/10.3389/fmicb.2025.1597514openalex-snapshot
Characterization, diversity, and biogeochemical potential of soil viruses inhabiting in Yuncheng Salt Lake
inferred← citeshttps://doi.org/10.3389/fpsyt.2021.722335openalex-snapshot
The Complex Molecular Picture of Gut and Oral Microbiota–Brain-Depression System: What We Know and What We Need to Know
inferred← citeshttps://doi.org/10.3390/antibiotics9100663openalex-snapshot
From Orphan Phage to a Proposed New Family–The Diversity of N4-Like Viruses
inferred← citeshttps://doi.org/10.3390/cimb47110906openalex-snapshot
Genomic and Biological Insights of Bacteriophage ΦBc24 Targeting Bacillus cereus
inferred← citeshttps://doi.org/10.3390/genes12020149openalex-snapshot
The Novel Halovirus Hardycor1, and the Presence of Active (Induced) Proviruses in Four Haloarchaea
inferred← citeshttps://doi.org/10.3390/ijms24054483openalex-snapshot
PCR Assay for Rapid Taxonomic Differentiation of Virulent Staphylococcus aureus and Klebsiella pneumoniae Bacteriophages
inferred← citeshttps://doi.org/10.3390/ijms252312885openalex-snapshot
In Vitro Susceptibility of Clinical and Carrier Strains of Staphylococcus aureus to STAFAL® Phage Preparation
inferred← citeshttps://doi.org/10.3390/microorganisms11082098openalex-snapshot
Phage-Based Biosensing for Rapid and Specific Detection of Staphylococcus aureus
inferred← citeshttps://doi.org/10.3390/microorganisms7100471openalex-snapshot
Characterization of the Three New Kayviruses and Their Lytic Activity Against Multidrug-Resistant Staphylococcus aureus
inferred← citeshttps://doi.org/10.3390/microorganisms8091374openalex-snapshot
Characterizing Phage-Host Interactions in a Simplified Human Intestinal Barrier Model
inferred← citeshttps://doi.org/10.3390/molecules29204889openalex-snapshot
Recent Progress in Terrestrial Biota Derived Antibacterial Agents for Medical Applications
inferred← citeshttps://doi.org/10.3390/v11010088openalex-snapshot
Design and Preclinical Development of a Phage Product for the Treatment of Antibiotic-Resistant Staphylococcus aureus Infections
inferred← citeshttps://doi.org/10.3390/v11070656openalex-snapshot
Human Virome and Disease: High-Throughput Sequencing for Virus Discovery, Identification of Phage-Bacteria Dysbiosis and Development of Therapeutic Approaches with Emphasis on the Human Gut
inferred← citeshttps://doi.org/10.3390/v12030292openalex-snapshot
A Kayvirus Distant Homolog of Staphylococcal Virulence Determinants and VISA Biomarker Is a Phage Lytic Enzyme
inferred← citeshttps://doi.org/10.3390/v12111268openalex-snapshot
VIRIDIC—A Novel Tool to Calculate the Intergenomic Similarities of Prokaryote-Infecting Viruses
inferred← citeshttps://doi.org/10.3390/v13030506openalex-snapshot
A Roadmap for Genome-Based Phage Taxonomy
inferred← citeshttps://doi.org/10.3390/v15010017openalex-snapshot
Phage K gp102 Drives Temperature-Sensitive Antibacterial Activity on USA300 MRSA
inferred← citeshttps://doi.org/10.3390/v15010076openalex-snapshot
Phage-Host Prediction Using a Computational Tool Coupled with 16S rRNA Gene Amplicon Sequencing
inferred← citeshttps://doi.org/10.3390/v15122287openalex-snapshot
Isolation and Characterization of New Bacteriophages against Staphylococcal Clinical Isolates from Diabetic Foot Ulcers
inferred← citeshttps://doi.org/10.47612/2226-3136-2021-13-83-102openalex-snapshot
SOME ASPECTS OF CURRENT BACTERIOPHAGES TAXONOMY
inferred← citeshttps://doi.org/10.6084/m9.figshare.14337756openalex-snapshot
Additional file 10 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes
inferred← citeshttps://doi.org/10.6084/m9.figshare.14337759openalex-snapshot
Additional file 11 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes
inferred← citeshttps://doi.org/10.6084/m9.figshare.14337762openalex-snapshot
Additional file 12 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes
inferred← citeshttps://doi.org/10.6084/m9.figshare.14337765openalex-snapshot
Additional file 13 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes
inferred← citeshttps://doi.org/10.6084/m9.figshare.14337768openalex-snapshot
Additional file 14 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes
inferred← citeshttps://doi.org/10.6084/m9.figshare.14337777openalex-snapshot
Additional file 4 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes
inferred← citeshttps://doi.org/10.6084/m9.figshare.14337786openalex-snapshot
Additional file 7 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes
inferred← citeshttps://doi.org/10.6084/m9.figshare.14337789openalex-snapshot
Additional file 8 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes
inferred← citeshttps://doi.org/10.6084/m9.figshare.14337792openalex-snapshot
Additional file 9 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes
inferred← citeshttps://doi.org/10.6084/m9.figshare.22612454openalex-snapshot
Additional file 1 of Genomic diversity and comprehensive taxonomical classification of 61 Bacillus subtilis group member infecting bacteriophages, and the identification of ortholog taxonomic signature genes
inferred← citeshttps://doi.org/10.6084/m9.figshare.22612457openalex-snapshot
Additional file 2 of Genomic diversity and comprehensive taxonomical classification of 61 Bacillus subtilis group member infecting bacteriophages, and the identification of ortholog taxonomic signature genes
inferred← citeshttps://doi.org/10.6084/m9.figshare.25414932openalex-snapshot
Additional file 1 of Isolation and characterization of lytic bacteriophages from various sources in Addis Ababa against antimicrobial-resistant diarrheagenic Escherichia coli strains and evaluation of their therapeutic potential
inferred← citeshttps://doi.org/10.70675/17b72026z076az4622za540z38bfb251dd02openalex-snapshot
Studying viral genome and protein diversity : bioinformatic developments and analysis of families of interest
inferred← citeshttps://doi.org/10.70675/291d4522zca29z4156z936ezdcea44fc811bopenalex-snapshot
Caractérisation du virome d’un écosystème tropical fortement anthropisé : la lagune Ebrié en Côte d’Ivoire
inferred← citeshttps://doi.org/10.70675/cbe2ca53z6c38z4615zafe0z731fbdda12a4openalex-snapshot
Bactériophages et vésicules extracellulaires du microbiote intestinal : développement de nouveaux outils d’étude et rôles dans les Maladies Inflammatoires Chroniques de l’Intestin (MICI)
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.