ArticleGenomics, proteomics & bioinformatics2015
CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy.
Article in Genomics, proteomics & bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers.
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78 citing papers in PubMed.
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- Complete genome and comparative analysis of Xanthomonas oryzae pv. oryzae isolated from northern Thailand.Access microbiology · 2025Article
- TreeWave: command line tool for alignment-free phylogeny reconstruction based on graphical representation of DNA sequences and genomic signal processing.BMC bioinformatics · 2024Article
- A novel hierarchical network-based approach to unveil the complexity of functional microbial genome.BMC genomics · 2024Article
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- Research on the targeted improvement of the yield of a new VBBMC biotechnology · 2023Article
- Trade-off in genome turnover events leading to adaptive evolution of Microcystis aeruginosa species complex.BMC genomics · 2023Article
- Comparative Genomic Analysis ofMicroorganisms · 2023Article
- Genomic diversity, pathogenicity and antimicrobial resistance of Escherichia coli isolated from poultry in the southern United States.BMC microbiology · 2023Article
- Distribution, characterization, and evolution of heavy metal resistance genes and Tn7-like associated heavy metal resistance Gene Island ofFrontiers in microbiology · 2023Article
- Low-toxinEmerging microbes & infections · 2022Article
- Genomic Characterization of Colistin-Resistant Isolates from the King Fahad Medical City, Kingdom of Saudi Arabia.Antibiotics (Basel, Switzerland) · 2022Article
- An accurate alignment-free protein sequence comparator based on physicochemical properties of amino acids.Scientific reports · 2022Article
18 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference and detailed comparison with taxonomy are great challenges. We now provide one solution in the latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3. The server resides in a cluster of 64 cores and is equipped with an interactive, collapsible, and expandable tree display. It is capable of comparing the tree branching order with prokaryotic classification at all taxonomic ranks from domains down to species and strains. CVTree3 allows for inquiry by taxon names and trial on lineage modifications. In addition, it reports a summary of monophyletic and non-monophyletic taxa at all ranks as well as produces print-quality subtree figures. After giving an overview of retrospective verification of the CVTree approach, the power of the new server is described for the mega-classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes. A few discrepancies between CVTree and 16S rRNA analyses are also summarized with regard to possible taxonomic revisions. CVTree3 is freely accessible to all users at http://tlife.fudan.edu.cn/cvtree3/ without login requirements.
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