CVTree protocols

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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 No
Maintained No

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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

 (11)
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, and cvtree oligopeptide profiling. sequenced strains of prochlorococcus marinus, of which phylogenetic relations have been discussed before, 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 (). blastp searches have been performed based on the whole amino acid sequences of s. lydicus 103 against those of other streptomyces genomes listed in with e-values less than 10−5. […]

2017
PMCID: 5381585
PMID: 28201618
DOI: 10.1093/gbe/evx024

[…] structures of proteins were predicted using the chou and fasman secondary structure prediction server (http://www.biogem.org/tool/chou-fasman/; last accessed january 11, 2017)., the web server cvtree3, which is an alignment- and parameter-free method that relies on the oligopeptide content (k-tuple length) of conserved proteins to deduce evolutionary relatedness (), was used […]

2016
PMCID: 4893749
PMID: 27264309
DOI: 10.1038/srep27572

[…] qiagen, usa) and sequenced on a pacbio rs ii platform. sequences were assembled into a complete chromosome by the hgap2.3.0 pipeline. annotation was performed by glimmer version3.02. we used the cvtree3.0 web server, which applies a composition vector to perform phylogenetic analysis, to construct a phylogenetic tree of bpb5 and reference genomes from the eztaxon database […]

2016
PMCID: 5117618
PMID: 27895706
DOI: 10.1186/s13068-016-0665-0

[…] results were downloaded from jgi and reformatted adding the latest go and e.c. ids. for 49 fungi the interpro results were already computed in [].a phylogenetic tree was built with cvtree using the protein sequences of all the organisms involved in the model reconstruction.a probabilistic model was built using the results of blast, gtg and the phylogenetic tree. conditional […]


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CVTree in publications

 (65)
PMCID: 5919953
PMID: 29731741
DOI: 10.3389/fmicb.2018.00746

[…] to evaluate the genome bins with a rating, and selected high-quality bins for genome reconstruction., to infer phylogenetic relationships among bacteria, a whole-genome-based and alignment-free composition vector tree (cvtree) method (xu and hao, ) was used to compare and cluster the genomes we extracted from our assemblies. distances were computed using the composition vector […]

PMCID: 5911508
PMID: 29713314
DOI: 10.3389/fmicb.2018.00711

[…] hgt. by testing on simulated bacterial sequences and real data sets with known horizontal transferred genomic regions, we found that more advanced alignment-free dissimilarity measures such as cvtree and d2* that take into account the background markov sequences can solve hgt detection problems with significantly improved performance. we also studied the influence of different factors […]

PMCID: 5897812
PMID: 29650568
DOI: 10.1128/genomeA.00210-18

[…] 3 rrnas, 1 transfer-messenger rna (tmrna), and 32 miscellaneous rnas. the genes involved in pathways were predicted by using the kegg automatic annotation server (kaas) (). based on the annotation, cvtree () was used to create a phylogenetic tree using the proteobacteria lineage, which consists of 1,043 genomes, including the paracoccus denitrificans genome., the strain istod1 genome harbored […]

PMCID: 5826093
PMID: 29511354
DOI: 10.1177/1176934318759299

[…] whole genome super-matrix trees in terms of tree topology when compared with other known approaches including 16s ribosomal rna and gyra protein sequence comparison, complete genome-based mauve, and cvtree methods. a web-based program to perform the alignment-free oup-based phylogenomic inferences was implemented at http://swphylo.bi.up.ac.za/. applicability of the tool was tested on different […]

PMCID: 5794947
PMID: 29437100
DOI: 10.1128/genomeA.01533-17

[…] of 69.84%. genome annotation using prokka () predicted 3,363 protein-coding sequences, 50 trnas, 4 rrnas, 1 transfer-messenger rna (tmrna), and 9 miscellaneous other rnas. based on the annotation, cvtree () was used to create a phylogenetic tree using the micrococcaceae lineage, which consists of 260 genomes, including the zhihengliuella sp. genome. the analysis reinforced the identification […]


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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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