Muscle (Alignment Software)

MUltiple Sequence Comparison by Log-Expectation
Original author(s)	Robert C. Edgar
Developer(s)	drive5
Initial release	2004; 20 years ago
Stable release	3.8.31 / 18 August 2016; 7 years ago
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]

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 $O(N 2 L + NL 2)$ , the space complexity is $O(N 2 + NL + L 2)$ . The refinement stage adds to the time complexity another term, $O(N 3 L)$ .^[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]

References

↑ ^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.
↑ ^2.0 ^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.
↑ "MUSCLE < Multiple Sequence Alignment < EMBL-EBI". http://www.ebi.ac.uk/Tools/msa/muscle/. Retrieved 1 September 2014.
↑ "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)

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[Edgar2004a-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.

[Edgar2004b-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.

[embl-ebi-3] "MUSCLE < Multiple Sequence Alignment < EMBL-EBI". http://www.ebi.ac.uk/Tools/msa/muscle/. Retrieved 1 September 2014.

[citations-4] "Robert C. Edgar - Google Scholar Citations". https://scholar.google.com/citations?user=RzVMRc0AAAAJ&hl=en. Retrieved 1 September 2016.

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

Muscle (Alignment Software)

Contents

Algorithm

Integration

See also

References

External links