{"name":"MUSCLE","description":"This tool performs multiple sequence alignments of nucleotide or amino acid sequences.","homepage":"https://www.drive5.com/muscle/","biotoolsID":"muscle","biotoolsCURIE":"biotools:muscle","version":["5"],"otherID":[],"relation":[],"function":[{"operation":[{"uri":"http://edamontology.org/operation_0492","term":"Multiple sequence alignment"}],"input":[{"data":{"uri":"http://edamontology.org/data_3494","term":"DNA sequence"},"format":[{"uri":"http://edamontology.org/format_1948","term":"nbrf/pir"},{"uri":"http://edamontology.org/format_1929","term":"FASTA"},{"uri":"http://edamontology.org/format_1935","term":"GCG"},{"uri":"http://edamontology.org/format_1997","term":"PHYLIP format"},{"uri":"http://edamontology.org/format_1927","term":"EMBL format"},{"uri":"http://edamontology.org/format_1936","term":"GenBank format"}]},{"data":{"uri":"http://edamontology.org/data_3495","term":"RNA sequence"},"format":[{"uri":"http://edamontology.org/format_1948","term":"nbrf/pir"},{"uri":"http://edamontology.org/format_1929","term":"FASTA"},{"uri":"http://edamontology.org/format_1935","term":"GCG"},{"uri":"http://edamontology.org/format_1997","term":"PHYLIP format"},{"uri":"http://edamontology.org/format_1927","term":"EMBL format"},{"uri":"http://edamontology.org/format_1936","term":"GenBank format"}]}],"output":[{"data":{"uri":"http://edamontology.org/data_0863","term":"Sequence alignment"},"format":[{"uri":"http://edamontology.org/format_1982","term":"ClustalW format"},{"uri":"http://edamontology.org/format_2331","term":"HTML"},{"uri":"http://edamontology.org/format_1997","term":"PHYLIP format"},{"uri":"http://edamontology.org/format_1947","term":"GCG MSF"},{"uri":"http://edamontology.org/format_1929","term":"FASTA"}]}],"note":null,"cmd":null}],"toolType":["Command-line tool","Web API"],"topic":[{"uri":"http://edamontology.org/topic_0080","term":"Sequence analysis"}],"operatingSystem":["Linux","Windows","Mac"],"language":[],"license":"Other","collectionID":["MUSCLE","galaxyPasteur","BioConductor"],"maturity":"Mature","cost":"Free of charge","accessibility":"Open access","elixirPlatform":[],"elixirNode":[],"elixirCommunity":[],"link":[{"url":"https://www.biocatalogue.org/services/3135","type":["Software catalogue"],"note":null},{"url":"https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/oneclick_phylogeny/muscle/3.8.31.1","type":["Galaxy service"],"note":null}],"download":[{"url":"http://bioconductor/packages/release/bioc/src/contrib/muscle_3.16.0.tar.gz","type":"Source code","note":"BioConductor package","version":null},{"url":"https://www.ebi.ac.uk/seqdb/confluence/display/WEBSERVICES/muscle_rest","type":"API specification","note":"EBI MUSCLE Web Service","version":null},{"url":"https://www.drive5.com/muscle/downloads.htm","type":"Downloads page","note":null,"version":null}],"documentation":[{"url":"http://bioconductor.org/packages/release/bioc/html/muscle.html","type":["User manual"],"note":"BioConductor package documentation"},{"url":"https://www.ebi.ac.uk/seqdb/confluence/display/WEBSERVICES/muscle_rest","type":["API documentation"],"note":"EBI Web Service documentation"},{"url":"https://www.drive5.com/muscle/manual/","type":["User manual"],"note":null},{"url":"https://www.drive5.com/muscle/manual/install.html","type":["Installation instructions"],"note":null}],"publication":[{"doi":"10.1093/nar/gkh340","pmid":"15034147","pmcid":"PMC390337","type":["Primary"],"version":null,"note":null,"metadata":{"title":"MUSCLE: Multiple sequence alignment with high accuracy and high throughput","abstract":"We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5.com/muscle. © Oxford University Press 20004; all rights reserved.","date":"2004-07-09T00:00:00Z","citationCount":34929,"authors":[{"name":"Edgar R.C."}],"journal":"Nucleic Acids Research"}},{"doi":"10.7490/f1000research.1114334.1","pmid":null,"pmcid":null,"type":["Primary"],"version":"5","note":null,"metadata":null},{"doi":"10.1186/1471-2105-5-113","pmid":"15318951","pmcid":"PMC517706","type":["Other"],"version":null,"note":null,"metadata":{"title":"MUSCLE: A multiple sequence alignment method with reduced time and space complexity","abstract":"Background: In a previous paper, we introduced MUSCLE, a new program for creating multiple alignments of protein sequences, giving a brief summary of the algorithm and showing MUSCLE to achieve the highest scores reported to date on four alignment accuracy benchmarks. Here we present a more complete discussion of the algorithm, describing several previously unpublished techniques that improve biological accuracy and / or computational complexity. We introduce a new option, MUSCLE-fast, designed for high-throughput applications. We also describe a new protocol for evaluating objective functions that align two profiles. Results: We compare the speed and accuracy of MUSCLE with CLUSTALW, Progressive POA and the MAFFT script FFTNS1, the fastest previously published program known to the author. Accuracy is measured using four benchmarks: BAliBASE, PREFAB, SABmark and SMART. We test three variants that offer highest accuracy (MUSCLE with default settings), highest speed (MUSCLEfast), and a carefully chosen compromise between the two (MUSCLE-prog). We find MUSCLE-fast to be the fastest algorithm on all test sets, achieving average alignment accuracy similar to CLUSTALW in times that are typically two to three orders of magnitude less. MUSCLE-fast is able to align 1,000 sequences of average length 282 in 21 seconds on a current desktop computer. Conclusions: MUSCLE offers a range of options that provide improved speed and / or alignment accuracy compared with currently available programs. MUSCLE is freely available at http:// www.drive5.com/muscle. © 2004 Edgar; licensee BioMed Central Ltd.","date":"2004-08-19T00:00:00Z","citationCount":6857,"authors":[{"name":"Edgar R.C."}],"journal":"BMC Bioinformatics"}},{"doi":"10.1101/2021.06.20.449169","pmid":null,"pmcid":null,"type":["Primary"],"version":"5","note":null,"metadata":null}],"credit":[{"name":"Alex T. Kalinka","email":"alex.t.kalinka@gmail.com","url":null,"orcidid":null,"gridid":null,"rorid":null,"fundrefid":null,"typeEntity":"Person","typeRole":["Maintainer"],"note":"Maintainer of the BioConductor package"},{"name":null,"email":null,"url":"http://www.ebi.ac.uk/support/","orcidid":null,"gridid":null,"rorid":null,"fundrefid":null,"typeEntity":"Person","typeRole":["Primary contact"],"note":"EBI Web Service support"},{"name":"Technical Support","email":null,"url":"https://www.drive5.com/muscle/manual/support.html","orcidid":null,"gridid":null,"rorid":null,"fundrefid":null,"typeEntity":null,"typeRole":[],"note":null},{"name":"Robert Edgar","email":"robert@drive5.com","url":null,"orcidid":null,"gridid":null,"rorid":null,"fundrefid":null,"typeEntity":"Person","typeRole":["Primary contact","Developer"],"note":null}],"owner":"bioconductor_import","additionDate":"2017-01-17T14:57:39Z","lastUpdate":"2024-11-24T20:10:00.504033Z","editPermission":{"type":"group","authors":["laurasansc"]},"validated":1,"homepage_status":0,"elixir_badge":0,"confidence_flag":null}