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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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