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

scientific article published on 20 May 2019

Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales is …
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scholarly articleQ13442814

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P356DOI10.1038/S41564-019-0448-Z
P698PubMed publication ID31110365

P50authorPhilip HugenholtzQ28219811
Donovan H ParksQ84300943
P2093author name stringSoo Jen Low
Mária Džunková
Pierre-Alain Chaumeil
P2860cites workResolving difficult phylogenetic questions: why more sequences are not enoughQ21092718
Toward Automatic Reconstruction of a Highly Resolved Tree of LifeQ22065877
The Phage Proteomic Tree: a genome-based taxonomy for phageQ24539335
The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophagesQ24555731
Genomic and genetic analysis of Bordetella bacteriophages encoding reverse transcriptase-mediated tropism-switching cassettesQ24599692
How discordant morphological and molecular evolution among microorganisms can revise our notions of biodiversity on EarthQ26991691
Using signature genes as tools to assess environmental viral ecology and diversityQ27006745
Uncovering Earth’s viromeQ27752340
A new view of the tree of lifeQ28005548
Increased taxon sampling greatly reduces phylogenetic errorQ28201637
IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogeniesQ28250973
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogeniesQ28658397
Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon samplingQ28728486
FastTree 2--approximately maximum-likelihood trees for large alignmentsQ28748616
Terrace Aware Data Structure for Phylogenomic Inference from SupermatricesQ28821932
Genome-scale approaches to resolving incongruence in molecular phylogeniesQ29547249
ARB: a software environment for sequence dataQ29547354
An approximately unbiased test of phylogenetic tree selectionQ29547508
Accelerated Profile HMM SearchesQ29547576
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analysesQ29547690
A phylogeny-driven genomic encyclopaedia of Bacteria and ArchaeaQ29616591
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaeaQ29617497
Universal trees based on large combined protein sequence data sets.Q30655328
Prospects for building the tree of life from large sequence databasesQ30772150
Inconsistency of phylogenetic estimates from concatenated data under coalescenceQ31105795
Missing data, incomplete taxa, and phylogenetic accuracyQ33187728
BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagramsQ33377261
The distribution and impact of viral lineages in domains of lifeQ33574667
vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and BacteriaQ33642282
Sparse supermatrices for phylogenetic inference: taxonomy, alignment, rogue taxa, and the phylogeny of living turtlesQ34119184
Increased taxon sampling is advantageous for phylogenetic inferenceQ34147941
Viral metagenomicsQ34417786
Consensus statement: Virus taxonomy in the age of metagenomicsQ34550236
Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatricesQ34701661
Understanding the enormous diversity of bacteriophages: the tailed phages that infect the bacterial family EnterobacteriaceaeQ34995724
Mosaic graphs and comparative genomics in phage communitiesQ35067223
Concatenated alignments and the case of the disappearing treeQ35535444
Linking Virus Genomes with Host Taxonomy.Q36735636
Integration of phenotypic metadata and protein similarity in Archaea using a spectral bipartitioning approachQ37169808
Characterization of bacteriophages Cp1 and Cp2, the strain-typing agents for Xanthomonas axonopodis pv. citriQ37545253
Characterization of novel virulent broad-host-range phages of Xylella fastidiosa and XanthomonasQ37545928
ModelFinder: fast model selection for accurate phylogenetic estimatesQ38798531
ViPTree: the viral proteomic tree serverQ38853376
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other treesQ39838204
ExaML version 3: a tool for phylogenomic analyses on supercomputersQ41145063
Diversity of prophages in dominant Staphylococcus aureus clonal lineages.Q41910627
Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophagesQ42628295
Bacteriophage genomicsQ43100161
Reticulate representation of evolutionary and functional relationships between phage genomesQ43581270
Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV).Q45326207
VICTOR: genome-based phylogeny and classification of prokaryotic virusesQ46284338
Using supermatrices for phylogenetic inquiry: an example using the sedgesQ46682719
Bacteriophage evolution differs by host, lifestyle and genome.Q47230329
Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee.Q47550438
Inferring species phylogenies from multiple genes: Concatenated sequence tree versus consensus gene treeQ56689215
Can Incomplete Taxa Rescue Phylogenetic Analyses from Long-Branch Attraction?Q57069712
More Genes or More Taxa? The Relative Contribution of Gene Number and Taxon Number to Phylogenetic AccuracyQ57162900
Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: steps towards a unified taxonomyQ59356725
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of lifeQ59543717
Molecular Genetics of MycobacteriophagesQ85450716
ape 5.0: an environment for modern phylogenetics and evolutionary analyses in RQ90281822
P433issue8
P304page(s)1306-1315
P577publication date2019-05-20
P1433published inNature MicrobiologyQ23022567
P1476titleEvaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales
P478volume4

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cites work (P2860)
Q92304163Charting the diversity of uncultured viruses of Archaea and Bacteria
Q97521132Computational approaches in viral ecology
Q92432604Defining the human gut host-phage network through single-cell viral tagging
Q90051707Global Organization and Proposed Megataxonomy of the Virus World
Q92453335New insights into intestinal phages
Q89768906Properties and abundance of overlapping genes in viruses
Q97522830The LUCA and its complex virome
Q92134914Towards a genome-based virus taxonomy

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