Clustal Omega protocols

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Clustal Omega specifications

Information


Unique identifier OMICS_00972
Name Clustal Omega
Alternative name ClustalOmega
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Information


Unique identifier OMICS_00972
Name Clustal Omega
Alternative name ClustalOmega
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publications for Clustal Omega

library_books

Clustal omega.

2014 Curr Protoc Bioinformatics
PMID: 25501942

Clustal Omega in pipelines

 (240)
2018
PMCID: 5759035
PMID: 29354144
DOI: 10.3389/fpls.2017.02191

[…] v8.1 (edgar, ) and rdp (cole et al., ) database (www.drive5.com/utax/rdp_16s.fa) with a confidence score of 0.9., phylogenetic analysis was performed by multiple alignments of cotu sequences using clustal omega v1.2.1 (sievers et al., ) with 1,000 iterations. a phylogenetic tree was constructed by maximum likelihood using qiime v1.8.0 (caporaso et al., ) and fasttree v2.1.3 (price et al., ). […]

2018
PMCID: 5770437
PMID: 29339766
DOI: 10.1038/s41598-018-19192-6

[…] an equal volume of dmso., the amino acid sequences of the enzymes were collected from the ncbi genebank. the sequence alignment was carried out using the online multiple sequence alignment tools clustal omega and macvector. the secondary structure analysis was carried out using the online tool stride. the alignment figure was created using aline. the superimposition of the crystal structures […]

2018
PMCID: 5777986
PMID: 29358647
DOI: 10.1038/s41598-018-19640-3

[…] from escherichia coli using blastp with cut-off e-value set to 1e-3. after removing incomplete entries, 3120 sequences were obtained. among them, the 111 enterobacterial homologues were aligned with clustal omega and the consensus sequence logo was plotted using weblogo3. the degree of sequence similarity of tat proteins between e. coli (tata, tate, tatb) and c. glutamicum (tata, tate, tatb) […]

2018
PMCID: 5785972
PMID: 29374183
DOI: 10.1038/s41467-018-02881-1

[…] local alignment search tool (blast) in national center for biotechnology information (ncbi) server using position-specific iterated blast (psi-blast) method. multiple alignment was performed by clustal omega. the evolutionary history was inferred by using the maximum likelihood method based on the le_gascuel_2008 model. the tree with the highest log likelihood (−13243.9235) is shown. […]

2018
PMCID: 5804921
PMID: 29378020
DOI: 10.1093/gbe/evy011

[…] and guanylate cyclases. the p. aurantium proteins harboring this domain were aligned with the five dictyostelium cyclases and a few signature ph. polycephalum and a. castellanii cyclases using clustal omega with five combined iterations (). after deletion of segments that did not align unambiguously, alignments were subjected to bayesian inference for phylogeny reconstruction using a mixed […]


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Clustal Omega in publications

 (1651)
PMCID: 5964351
DOI: 10.1128/mBio.00869-18

[…] 2obt) () and hunov gii.4.2012/nsw0514 bound to type a trisaccharide (pdb id: 4wzt) () and mnv (pdb id: 3lqe) structures from the protein data bank. the amino acid sequences were aligned using the clustal omega platform on the bioinformatics toolkit from the max planck institute (, ). the predicted tertiary structure of the aligned sequence was determined by the use of the modeller platform […]

PMCID: 5956151
PMID: 29769380
DOI: 10.1128/mSphere.00165-18

[…] tcs08 and the staphylococcal saers systems. the red residues indicate the reported histidine and aspartate residues for saes and saer, respectively. the sequence comparison was performed using the clustal omega tool from the embl-ebi, and the protein sequences were retrieved using the kyoto encyclopedia of genes and genomes (kegg). the asterisk indicates a score of 1, the colon indicates […]

PMCID: 5945626
PMID: 29748565
DOI: 10.1038/s41467-018-03917-2

[…] using the ensembl variant effect predictor rest api (implementation: github.com/genefunctionteam/bioruby-sam-mutation). sequences were also translated and multiple alignments generated using clustal omega (http://www.ebi.ac.uk/tools/msa/clustalo/). for the dense screen, coverage was calculated per base using samtools pileup (github.com/samtools, v1.5) with a maximum depth of 300,000., […]

PMCID: 5943310
PMID: 29743617
DOI: 10.1038/s41598-018-25463-z

[…] based on bbo2 rdna sequence (http://biology.unm.edu/biomphalaria-genome/rdnabg.html)., sequence alignments and percent identity of nucleotides (nt) and amino acids (aa) were determined using clustal omega (https://www.ebi.ac.uk/tools/msa/clustalo/). heat-maps of pair-wise sequence identities were generated using the r package ggplot2. evolutionary rate including synonymous, […]

PMCID: 5943489
PMID: 29774014
DOI: 10.3389/fmicb.2018.00862

[…] v14.5, homd refseq extended v1.1, modified greengenegold, and the ncbi's microbial 16s set (al-hebshi et al., , ). taxonomy classification was also assigned according to the greengenes database. clustal omega software was used to construct phylogenetic trees from the representative sequences of the otus. the α-diversity (e.g., observed otu numbers, chao index, simpson index, and shannon […]


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Clustal Omega institution(s)
School of Medicine and Medical Science, Conway Institute, University College Dublin, Ireland

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