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

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.

Pubmed ID: 15034147


  • Edgar RC


Nucleic acids research

Publication Data

March 22, 2004

Associated Grants


Mesh Terms

  • Algorithms
  • Amino Acid Motifs
  • Amino Acid Sequence
  • Internet
  • Molecular Sequence Data
  • Reproducibility of Results
  • Sequence Alignment
  • Sequence Analysis, Protein
  • Software
  • Time Factors