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Published online 19 March 2004
Nucleic Acids Research, 2004, Vol. 32, No. 5 1792-1797
Oxford University Press
MUSCLE: multiple sequence alignment with high accuracy and high throughput
195 Roque Moraes Drive, Mill Valley, CA 94941, USA
*Email: bob{at}drive5.com
Received January 19, 2004; Revised January 30, 2004; Accepted February 24, 2004
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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C.-H. Kuo, N. A. Moran, and H. Ochman The consequences of genetic drift for bacterial genome complexity Genome Res., August 1, 2009; 19(8): 1450 - 1454. [Abstract] [Full Text] [PDF]
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F. Zhao, J. Qi, and S. C. Schuster Tracking the past: Interspersed repeats in an extinct Afrotherian mammal, Mammuthus primigenius Genome Res., August 1, 2009; 19(8): 1384 - 1392. [Abstract] [Full Text] [PDF]
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J. H. Fong and A. Marchler-Bauer CORAL: aligning conserved core regions across domain families Bioinformatics, August 1, 2009; 25(15): 1862 - 1868. [Abstract] [Full Text] [PDF]
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A. F. Neuwald Rapid detection, classification and accurate alignment of up to a million or more related protein sequences Bioinformatics, August 1, 2009; 25(15): 1869 - 1875. [Abstract] [Full Text] [PDF]
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R. Gouveia-Oliveira, F. S. Roque, R. Wernersson, T. Sicheritz-Ponten, P. W. Sackett, A. Molgaard, and A. G. Pedersen InterMap3D: predicting and visualizing co-evolving protein residues Bioinformatics, August 1, 2009; 25(15): 1963 - 1965. [Abstract] [Full Text] [PDF]
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S. T. Mugford, X. Qi, S. Bakht, L. Hill, E. Wegel, R. K. Hughes, K. Papadopoulou, R. Melton, M. Philo, F. Sainsbury, et al. A Serine Carboxypeptidase-Like Acyltransferase Is Required for Synthesis of Antimicrobial Compounds and Disease Resistance in Oats PLANT CELL, August 1, 2009; 21(8): 2473 - 2484. [Abstract] [Full Text] [PDF]
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C. Staiger, A. Hinneburg, and R. B. Klosgen Diversity in Degrees of Freedom of Mitochondrial Transit Peptides Mol. Biol. Evol., August 1, 2009; 26(8): 1773 - 1780. [Abstract] [Full Text] [PDF]
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J. R.P.M. Strating, N. H.M. van Bakel, J. A.M. Leunissen, and G. J.M. Martens A Comprehensive Overview of the Vertebrate p24 Family: Identification of a Novel Tissue-Specifically Expressed Member Mol. Biol. Evol., August 1, 2009; 26(8): 1707 - 1714. [Abstract] [Full Text] [PDF]
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R. P. Meisel, M. V. Han, and M. W. Hahn A Complex Suite of Forces Drives Gene Traffic from Drosophila X Chromosomes Gen Biol Evol, July 31, 2009; 2009(0): 176 - 188. [Abstract] [Full Text] [PDF]
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C.-H. Kuo and H. Ochman Deletional Bias across the Three Domains of Life Gen Biol Evol, July 10, 2009; 2009(0): 145 - 152. [Abstract] [Full Text] [PDF]
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M. Balke, I. Ribera, L. Hendrich, M. A. Miller, K. Sagata, A. Posman, A. P. Vogler, and R. Meier New Guinea highland origin of a widespread arthropod supertramp Proc R Soc B, July 7, 2009; 276(1666): 2359 - 2367. [Abstract] [Full Text] [PDF]
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