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MUSCLE | Multiple sequence alignment with high throughput

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A 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.

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MUSCLE classification

MUSCLE specifications

Unique identifier:
OMICS_00982
Interface:
Web user interface
Computer skills:
Basic
Maintained:
Yes
Name:
MUltiple Sequence Comparison by Log- Expectation
Restrictions to use:
None
Stability:
Stable

MUSCLE support

Maintainer

  • Rodrigo Lopez <>

Credits

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Publications

Institution(s)

EMBL Outstation–European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK

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