Clustal Omega protocols

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

 (109)
2018
PMCID: 5777986
PMID: 29358647
DOI: 10.1038/s41598-018-19640-3

[…] escherichia coli using blastp49 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 omega50 and the consensus sequence logo was plotted using weblogo351. 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 model43. the tree with the highest log likelihood (−13243.9235) is shown. […]

2018
PMCID: 5805349
PMID: 29420618
DOI: 10.1371/journal.pone.0192653

[…] i, iv, v, and vi as search set was applied. blastn and tblastn options were selected with the nucleotide collection (nr/nt). a multiple sequence alignment of selected proteins was performed with the clustal omega sequence alignment tool. the amino acid sequences of (putative) khs enzymes from f. solani (aaa87627.1), n. haematococca. (xp_003041184), aspergillus terreus (xp_001217367) […]

2018
PMCID: 5806211
PMID: 29435494
DOI: 10.1128/mSphereDirect.00011-18

[…] acid sequences (table 1) were obtained from genbank in fasta format with a preference for whole-genome sequences partitioned into designated mature peptides. the sequences were aligned using the clustal omega multiple sequence alignment (msa) server maintained by the european molecular biology laboratory’s european bioinformatics institute (embl-ebi). a phylogenetic tree was then generated […]

2018
PMCID: 5823468
PMID: 29425229
DOI: 10.1371/journal.ppat.1006870

[…] the conserved domain database search (cdd-search) from the ncbi site was used to compare motif identity and similarity with known conserved domains [55]. sequence alignments were obtained by using clustal omega software [56], edited using bioedit and refined using boxshade. the physical-chemical properties of the deduced protein were determined by the protein machine software available […]

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

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