MUSCLE (alignment software)

MUltiple Sequence Comparison by Log-ExpectationOriginal author(s)| Robert C. Edgar

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Developer(s)| drive5
Initial release| 2004; 22 years ago (2004)
Stable release|

3.8.31 / 18 August 2016; 9 years ago (2016-08-18)

Operating system| Linux, macOS, Windows
Platform| IA-32, x86-64
Available in| English
Type| Multiple sequence alignment
License| Public domain
Website| www.drive5.com/muscle

MUltiple Sequence Comparison by Log-Expectation (MUSCLE) is computer software for multiple sequence alignment of protein and nucleotide sequences. It is licensed as public domain. The method was published by Robert C. Edgar in two papers in 2004. The first paper, published in Nucleic Acids Research, introduced the sequence alignment algorithm.[1] The second paper, published in BMC Bioinformatics, presented more technical details.[2]

## Contents

* 1 Algorithm
* 2 Integration
* 3 See also
* 4 References
* 5 External links

## Algorithm

The MUSCLE algorithm proceeds in three stages: the draft progressive, improved progressive, and refinement stages. In the draft progressive stage, the algorithm produces a draft multiple alignment, emphasising speed over accuracy. In the improved progressive stage, the Kimura distance is used to reestimate the binary tree to create the draft alignment, in turn producing a more accurate multiple alignment. The final refinement stage refines the improved alignment made in step two. Multiple alignments are available at the end of each stage. In the first two stages of the algorithm, the time complexity is O(N2L \+ NL2), the space complexity is O(N2 \+ NL \+ L2). The refinement stage adds to the time complexity another term, O(N3L).[1] MUSCLE is often used as a replacement for Clustal, since it usually (but not always) gives better sequence alignments, depending on the chosen options. Also, MUSCLE is significantly faster than Clustal, more so for larger alignments.[1][2]

## Integration

MUSCLE is integrated into DNASTAR's Lasergene software, Geneious, and MacVector and is available in Sequencher, MEGA, and UGENE as a plug-in. MUSCLE is also available as a web service via the European Molecular Biology Laboratory (EMBL)-European Bioinformatics Institute (EBI).[3] As of September 2016, the two papers describing MUSCLE have been cited more than 19,000 times in total.[4]

## See also

* Sequence alignment software
* DNASTAR
* Clustal
* ProbCons
* AMAP
* T-COFFEE
* MAFFT

## References

1. ↑ 1.0 1.1 1.2 Edgar RC (2004). "MUSCLE: multiple sequence alignment with high accuracy and high throughput". Nucleic Acids Research 32 (5): 1792–97. doi:10.1093/nar/gkh340. PMID 15034147.
2. ↑ 2.0 2.1 Edgar RC (2004). "MUSCLE: a multiple sequence alignment method with reduced time and space complexity". BMC Bioinformatics 5 (1): 113. doi:10.1186/1471-2105-5-113. PMID 15318951.
3. ↑ "MUSCLE < Multiple Sequence Alignment < EMBL-EBI". http://www.ebi.ac.uk/Tools/msa/muscle/. Retrieved 1 September 2014.
4. ↑ "Robert C. Edgar - Google Scholar Citations". https://scholar.google.com/citations?user=RzVMRc0AAAAJ&hl=en. Retrieved 1 September 2016.

## External links

* MUSCLE Web Server (EMBL-EBI)

* v
* t
* e

Bioinformatics

Databases|

* Sequence databases: GenBank, European Nucleotide Archive and DNA Data Bank of Japan
* Secondary databases: UniProt, database of protein sequences grouping together Swiss-Prot, TrEMBL and Protein Information Resource
* Other databases: Protein Data Bank, Ensembl and InterPro
* Specialised genomic databases: BOLD, Saccharomyces Genome Database, FlyBase]], VectorBase]], WormBase, PHI-base, Arabidopsis Information Resource and Zebrafish Information Network

Software|

* BLAST
* Bowtie
* Clustal
* HMMER
* MUSCLE
* SAMtools
* TopHat

Other|

* Server: ExPASy
* Ontology: Gene Ontology
* Rosalind (education platform)

Institutions|

* Broad Institute
* Computational Biology Department (CBD)
* Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI)
* Database Center for Life Science (DBCLS)
* DNA Data Bank of Japan (DDBJ)
* European Bioinformatics Institute (EMBL-EBI)
* European Molecular Biology Laboratory (EMBL)
* Flatiron Institute
* J. Craig Venter Institute (JCVI)
* Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)
* US National Center for Biotechnology Information (NCBI)
* Japanese Institute of Genetics
* Netherlands Bioinformatics Centre (NBIC)
* Philippine Genome Center (PGC)
* Scripps Research
* Swiss Institute of Bioinformatics (SIB)
* Wellcome Sanger Institute
* Whitehead Institute

Organizations|

* African Society for Bioinformatics and Computational Biology (ASBCB)
* Australia Bioinformatics Resource (EMBL-AR)
* European Molecular Biology network (EMBnet)
* International Nucleotide Sequence Database Collaboration (INSDC)
* International Society for Biocuration (ISB)
* International Society for Computational Biology (ISCB)
* Student Council (ISCB-SC)
* Institute of Genomics and Integrative Biology (CSIR-IGIB)
* Japanese Society for Bioinformatics (JSBi)

Meetings|

* Basel Computational Biology Conference‎ ([BC2])
* European Conference on Computational Biology (ECCB)
* Intelligent Systems for Molecular Biology (ISMB)
* International Conference on Bioinformatics (InCoB)
* ISCB Africa ASBCB Conference on Bioinformatics
* Pacific Symposium on Biocomputing (PSB)
* Research in Computational Molecular Biology (RECOMB)

File formats|

* CRAM format
* FASTA format
* FASTQ format
* NeXML format
* Nexus format
* Pileup format
* SAM format
* Stockholm format

Related topics|

* Computational biology
* List of biological databases
* Molecular phylogenetics
* Sequencing
* Sequence database
* Sequence alignment

* Category
* Commons

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