MUSCLE: multiple sequence alignment with high accuracy and high throughput

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ID: 289061
2004
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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.
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openalex_W2132926880 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors R. C. Edgar
Journal Nucleic Acids Research
Year 2004
DOI
10.1093/nar/gkh340
URL
https://academic.oup.com/nar/article-pdf/32/5/1792/7055030/gkh340.pdf
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