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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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H. Liu, I. Probert, J. Uitz, H. Claustre, S. Aris-Brosou, M. Frada, F. Not, and C. de Vargas Extreme diversity in noncalcifying haptophytes explains a major pigment paradox in open oceans PNAS, August 4, 2009; 106(31): 12803 - 12808. [Abstract] [Full Text] [PDF]
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D. L. Adelson, J. M. Raison, and R. C. Edgar Characterization and distribution of retrotransposons and simple sequence repeats in the bovine genome PNAS, August 4, 2009; 106(31): 12855 - 12860. [Abstract] [Full Text] [PDF]
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J. Zielonka, I. G. Bravo, D. Marino, E. Conrad, M. Perkovic, M. Battenberg, K. Cichutek, and C. Munk Restriction of Equine Infectious Anemia Virus by Equine APOBEC3 Cytidine Deaminases J. Virol., August 1, 2009; 83(15): 7547 - 7559. [Abstract] [Full Text] [PDF]
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W. F. Fricke, T. J. Welch, P. F. McDermott, M. K. Mammel, J. E. LeClerc, D. G. White, T. A. Cebula, and J. Ravel Comparative Genomics of the IncA/C Multidrug Resistance Plasmid Family J. Bacteriol., August 1, 2009; 191(15): 4750 - 4757. [Abstract] [Full Text] [PDF]
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Z. Wunderlich and L. A. Mirny Using genome-wide measurements for computational prediction of SH2-peptide interactions Nucleic Acids Res., August 1, 2009; 37(14): 4629 - 4641. [Abstract] [Full Text] [PDF]
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M. E. Siddall, F. M. Fontanella, S. C. Watson, S. Kvist, and C. Erseus Barcoding Bamboozled by Bacteria: Convergence to Metazoan Mitochondrial Primer Targets by Marine Microbes Syst Biol, August 1, 2009; 58(4): 445 - 451. [Full Text] [PDF]
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N. C. Sheffield, H. Song, S. L. Cameron, and M. F. Whiting Nonstationary Evolution and Compositional Heterogeneity in Beetle Mitochondrial Phylogenomics Syst Biol, August 1, 2009; 58(4): 381 - 394. [Abstract] [Full Text] [PDF]
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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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 B. Jacobs, F. Lens, and E. Smets Evolution of fruit and seed characters in the Diervilla and Lonicera clades (Caprifoliaceae, Dipsacales) Ann. Bot., August 1, 2009; 104(2): 253 - 276. [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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