{"name":"Clustal Omega","description":"Multiple sequence alignment software. The name is occassionally spelled as ClustalOmega, Clustal Ω, ClustalΩ, Clustal O, ClustalO.","homepage":"http://www.clustal.org/omega/","biotoolsID":"clustalo","biotoolsCURIE":"biotools:clustalo","version":["1.0 - 1.2"],"otherID":[],"relation":[],"function":[{"operation":[{"uri":"http://edamontology.org/operation_0492","term":"Multiple sequence alignment"}],"input":[{"data":{"uri":"http://edamontology.org/data_2044","term":"Sequence"},"format":[{"uri":"http://edamontology.org/format_1929","term":"FASTA"}]}],"output":[{"data":{"uri":"http://edamontology.org/data_0863","term":"Sequence alignment"},"format":[{"uri":"http://edamontology.org/format_1929","term":"FASTA"}]}],"note":null,"cmd":null}],"toolType":["Command-line tool","Library"],"topic":[{"uri":"http://edamontology.org/topic_0080","term":"Sequence analysis"}],"operatingSystem":["Linux","Windows","Mac"],"language":[],"license":"GPL-2.0","collectionID":["clustal","Bioconda","galaxyPasteur","DebianMed"],"maturity":"Mature","cost":"Free of charge","accessibility":"Open access","elixirPlatform":[],"elixirNode":[],"elixirCommunity":[],"link":[{"url":"https://galaxy.pasteur.fr/?tool_id=toolshed.pasteur.fr%2Frepos%2Fdcorreia%2Fclustalo%2Fclustalo%2F1.2.1.1&version=1.2.1.1&__identifer=9si4ugr4fwu","type":["Galaxy service"],"note":null},{"url":"http://bioinf.ucd.ie/bugzilla/buglist.cgi?quicksearch=clustal","type":["Issue tracker"],"note":null}],"download":[{"url":"http://www.clustal.org/omega/#Download","type":"Downloads page","note":null,"version":null},{"url":"https://tracker.debian.org/pkg/clustalo","type":"Software package","note":"Debian package (Debian Med Packaging Team). Source code package 'clustalo' and binary packages including API and its documentation.","version":null},{"url":"https://bioconda.github.io/recipes/clustalo/README.html","type":"Software package","note":"Conda package (Bioconda channel). Conda recipe at https://github.com/bioconda/bioconda-recipes/tree/master/recipes/clustalo/meta.yaml","version":null}],"documentation":[{"url":"http://www.clustal.org/omega/#Documentation","type":["General"],"note":null},{"url":"http://www.clustal.org/omega/README","type":["User manual"],"note":"Clustal README file"},{"url":"http://www.clustal.org/omega/INSTALL","type":["Installation instructions"],"note":null}],"publication":[{"doi":"10.1038/msb.2011.75","pmid":"21988835","pmcid":"PMC3261699","type":["Primary"],"version":null,"note":null,"metadata":{"title":"Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega","abstract":"Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis pipelines when faced with data sets of the size of many thousands of sequences. Some methods allow computation of larger data sets while sacrificing quality, and others produce high-quality alignments, but scale badly with the number of sequences. In this paper, we describe a new program called Clustal Omega, which can align virtually any number of protein sequences quickly and that delivers accurate alignments. The accuracy of the package on smaller test cases is similar to that of the high-quality aligners. On larger data sets, Clustal Omega outperforms other packages in terms of execution time and quality. Clustal Omega also has powerful features for adding sequences to and exploiting information in existing alignments, making use of the vast amount of precomputed information in public databases like Pfam. © 2011 EMBO and Macmillan Publishers Limited All rights reserved.","date":"2011-10-19T00:00:00Z","citationCount":11023,"authors":[{"name":"Sievers F."},{"name":"Wilm A."},{"name":"Dineen D."},{"name":"Gibson T.J."},{"name":"Karplus K."},{"name":"Li W."},{"name":"Lopez R."},{"name":"McWilliam H."},{"name":"Remmert M."},{"name":"Soding J."},{"name":"Thompson J.D."},{"name":"Higgins D.G."}],"journal":"Molecular Systems Biology"}},{"doi":"10.1002/pro.3290","pmid":"28884485","pmcid":"PMC5734385","type":["Primary"],"version":null,"note":null,"metadata":{"title":"Clustal Omega for making accurate alignments of many protein sequences","abstract":"Clustal Omega is a widely used package for carrying out multiple sequence alignment. Here, we describe some recent additions to the package and benchmark some alternative ways of making alignments. These benchmarks are based on protein structure comparisons or predictions and include a recently described method based on secondary structure prediction. In general, Clustal Omega is fast enough to make very large alignments and the accuracy of protein alignments is high when compared to alternative packages. The package is freely available as executables or source code from www.clustal.org or can be run on-line from a variety of sites, especially the EBI www.ebi.ac.uk.","date":"2018-01-01T00:00:00Z","citationCount":1148,"authors":[{"name":"Sievers F."},{"name":"Higgins D.G."}],"journal":"Protein Science"}},{"doi":"10.1002/0471250953.bi0313s48","pmid":"25501942","pmcid":null,"type":["Usage"],"version":null,"note":"How to use Clustal Omega. Not open access.","metadata":{"title":"Clustal Omega","abstract":"Clustal Omega is a package for making multiple sequence alignments of amino acid or nucleotide sequences, quickly and accurately. It is a complete upgrade and rewrite of earlier Clustal programs. This unit describes how to run Clustal Omega interactively from a command line, although it can also be run online from several sites. The unit describes a basic protocol for taking a set of unaligned sequences and producing a full alignment. There are also protocols for using an external HMM or iteration to help improve an alignment.","date":"2014-01-01T00:00:00Z","citationCount":414,"authors":[{"name":"Sievers F."},{"name":"Higgins D.G."}],"journal":"Current Protocols in Bioinformatics"}}],"credit":[{"name":"Clustal helpdesk","email":"clustalw@ucd.ie","url":null,"orcidid":null,"gridid":null,"rorid":null,"fundrefid":null,"typeEntity":"Division","typeRole":["Primary contact"],"note":null},{"name":"Science Foundation Ireland","email":null,"url":"http://www.sfi.ie/","orcidid":null,"gridid":null,"rorid":null,"fundrefid":null,"typeEntity":"Funding agency","typeRole":[],"note":null}],"owner":"hmenager","additionDate":"2016-12-19T14:28:44Z","lastUpdate":"2024-11-24T20:19:47.776845Z","editPermission":{"type":"private","authors":[]},"validated":1,"homepage_status":0,"elixir_badge":0,"confidence_flag":null}