CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy
| Autor: | Bailin Hao, Guanghong Zuo |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2015 |
| Předmět: |
Web server
Biology computer.software_genre Biochemistry Genome Monophyly Phylogenetics Genome Archaeal RNA Ribosomal 16S Application Note Genetics Taxonomic rank Alignment-free phylogeny lcsh:QH301-705.5 Molecular Biology Phylogeny Retrospective Studies Internet Information retrieval Bacteria Ecology Archaea and Bacteria taxonomy Archaea Computational Mathematics Tree (data structure) Taxon lcsh:Biology (General) CVTree Whole-genome-based tree Taxonomy (biology) computer Sequence Alignment Composition vector Genome Bacterial |
| Zdroj: | Genomics, Proteomics & Bioinformatics Genomics, Proteomics & Bioinformatics, Vol 13, Iss 5, Pp 321-331 (2015) |
| ISSN: | 2210-3244 1672-0229 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|