CVTree pipeline

CVTree specifications

Information


Unique identifier OMICS_06237
Name CVTree
Alternative names Composition Vector Tree, CVTree3
Interface Web user interface
Restrictions to use None
Input data Some amino acid or nucleotide sequences.
Input format FASTA
Output data A distance matrix and tree files.
Computer skills Basic
Version 3.0
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Guanghong Zuo <>
  • person_outline Bailin Hao <>

Additional information


http://tlife.fudan.edu.cn/cvtree/cvtree3/manual/manual.html http://bigd.big.ac.cn/cvtree/cvtree3/

Publications for Composition Vector Tree

CVTree IN pipelines

 (3)
2018
PMCID: 5826093
PMID: 29511354
DOI: 10.1177/1176934318759299

[…] innovative phylogenetic approaches such as the super-matrix concatenation of alignments of orthologous gene sequences, 16s ribosomal rna (rrna) phylogenetics, mauve whole genome alignment,28 and cvtree oligopeptide profiling.29 sequenced strains of prochlorococcus marinus, of which phylogenetic relations have been discussed before,30 were used as a case study to test consistency of the oup […]

2017
PMCID: 5357945
PMID: 28317865
DOI: 10.1038/srep44786

[…] chromosome of s. lydicus 103 in this study is circular, which may lead to more genetic stability. phylogenetic analysis of s. lydicus 103 with other streptomyces species has been carried out using cvtree (fig. s2). blastp searches have been performed based on the whole amino acid sequences of s. lydicus 103 against those of other streptomyces genomes listed in fig. s2 with e-values less […]

2013
PMCID: 3686770
PMID: 23840352
DOI: 10.1371/journal.pone.0065670

[…] comparison was done with the top hit of the comparative genome analysis (s. pneumoniae r6) and the closely related s. mitis nctc12261. the whole genome phylogenetic analysis was conducted using the cvtree platform [16]., to verify the presence of locus sppn_05425 in all isolates (copy 1 of lyta which contains the v317r polymorphism) as well as to perform bidirectional sanger sequencing […]

CVTree institution(s)
T-Life Research Center, Department of Physics, Fudan University, Shanghai, China
CVTree funding source(s)
Supported by the National Basic Research Program of the Ministry of Science and Technology of China (973 Project; Grant No. 2013CB834100) and the State Key Laboratory of Applied Surface Physics as well as the Department of Physics, Fudan University, China.

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