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MUSCLE: multiple sequence alignment with high accuracy and high throughput.

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Nucleic acids research

Oxford University Press (OUP)

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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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      Author and article information

      Affiliations
      [1 ] bob@drive5.com
      Journal
      Nucleic Acids Res.
      Nucleic acids research
      Oxford University Press (OUP)
      1362-4962
      0305-1048
      2004
      : 32
      : 5
      15034147
      10.1093/nar/gkh340
      32/5/1792
      390337

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