Clustal W protocols

View Clustal W computational protocol

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Clustal W specifications

Information


Unique identifier OMICS_02562
Name Clustal W
Alternative names Clustal X, ClustalX, ClustalW, ClustalW2, ClustalX2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Clustal W/Clustal X Team <>

Information


Unique identifier OMICS_02562
Name Clustal W
Alternative names Clustal X, ClustalX, ClustalW, ClustalW2, ClustalX2
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Clustal W/Clustal X Team <>

Publication for Clustal W

Clustal W in pipelines

 (3663)
2018
PMCID: 5907373
PMID: 29669586
DOI: 10.1186/s12985-018-0981-z

[…] between the viral contigs were sequenced by pcr. the genomic ends were analyzed by 5′ and 3′ race pcrs. the orf was predicted with the ncbi orf finder. the conserved domains were identified with clustalw multiple sequence alignment, and a phylogenetic tree was built with mega. the presence of the virus in individual mosquito pools was detected by rt-pcr assay., a near full-length viral […]

2018
PMCID: 5818429
PMID: 29497429
DOI: 10.3389/fpls.2018.00166

[…] figure s1 | amino acid sequence alignment and pspg box of csugt76f1 and six homologies. the multiple alignment was performed using clustalw2 software. pspg box logo was produced by using meme software (http://meme-suite.org) ()., table s1 | primers sequences used in experiments., table s2 | identification of flavonoids in fruit […]

2018
PMCID: 5818486
PMID: 29459728
DOI: 10.1038/s41598-018-21679-1

[…] (np_001120822). multiple sequence alignment of med18 in tomato with other species was conducted by dnaman 6.0 programs. alignments of amino acid sequences of med18 subunits proteins were made using clustal x2.1. a phylogenetic tree of mediator of rna polymerase ii transcription subunit 18 protein sequence in 7 different species was constructed using mega7 (http://megasoftware.net/) […]

2018
PMCID: 5907808
PMID: 28940727
DOI: 10.1111/irv.12485

[…] genome segments were assembled using seqman version 14.1.0 (118) 412, dnastar, madison, wi. multiple nucleotide, and amino acid sequence alignments of each segment were constructed using the clustalw accessory application in bioedit sequence alignment editor version 7.2.5. maximum‐likelihood phylogenetic trees were constructed using mega7 version 7.0.14 with ha1 and na gene sequences […]

2018
PMCID: 5908059
PMID: 29672525
DOI: 10.1371/journal.pone.0194792

[…] and scanprosite (http://prosite.expasy.org/scanprosite/) and ncbi cdd (http://www.ncbi.nlm.nih.gov/structure/cdd/wrpsb.cgi)., protein members of the cluster sequences were aligned using two methods, clustalw [] and mafft version 7 []. in order to get an overview of the relationships between selected orthologous genes, phylogenetic trees were constructed using molecular evolutionary genetics […]


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Clustal W in publications

 (18152)
PMCID: 5958079
PMID: 29773850
DOI: 10.1038/s41598-018-26180-3

[…] cells. transconjugants were evaluated by in situ gel electrophoresis type gels. co-integrates were never visualized in any of the experiments performed., protein alignments were carried out using clustalw default parameters. plasmids were classified according to their relaxase proteins as described by garcillán-barcia et al.. mob families and subfamilies were also defined […]

PMCID: 5955974
PMID: 29769530
DOI: 10.1038/s41426-018-0087-0

[…] hiv-1 backbone (psg3△env). the culture supernatants were used to infect tzm-bl cells. env clones conferring the highest infectivity were selected for further study., sequences were aligned using the clustalw program in mega 6.06 software. phylogenetic analysis was conducted using the neighbor-joining method. glycosylation sites were predicted with the hiv-1 database online program n-glycosite […]

PMCID: 5956068
PMID: 29769532
DOI: 10.1038/s41467-018-04273-x

[…] each gene from each sea urchin, and the primer sequences were excluded for prior to the sequence alignments. the nucleotide sequences for each gene were first aligned within each s. purpuratus using clustalw (www.genome.jp/tools/clustalw), and the dominant sequences corresponding to the two alleles were then selected for subsequently comparison between individual sea urchins., complementary dna […]

PMCID: 5955947
PMID: 29769540
DOI: 10.1038/s41598-018-24974-z

[…] (lkcm01000102, jmiy01000002 and fzmp01000185) and 28 mcra partial sequences of m. nitroreducens-like archaea (kx290017-kx290044) were downloaded. the alignment of these sequences was performed with clustal x (version 2.0) and the conserved region was selected as the target for the primer design (fig. ). the primer design was then carried out using primer premier (version 6.0, premier biosoft […]

PMCID: 5951878
PMID: 29780684
DOI: 10.1007/s13721-018-0166-0

[…] tool) (altshul et al. ) at the ncbi and the homologous entries were obtained from the protein data bank (berman et al. ). the blastp alignment was further refined using sequence alignments in the clustal w/x 1.83 with default parameters (thompson et al. )., the blastp alignment was used for homology modeling built in modeller9v3 (http://www.salilab.org/modeller/9v3) which generated structures […]


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Clustal W institution(s)
The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland

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