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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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P. A. Beare, N. Unsworth, M. Andoh, D. E. Voth, A. Omsland, S. D. Gilk, K. P. Williams, B. W. Sobral, J. J. Kupko III, S. F. Porcella, et al. Comparative Genomics Reveal Extensive Transposon-Mediated Genomic Plasticity and Diversity among Potential Effector Proteins within the Genus Coxiella Infect. Immun., February 1, 2009; 77(2): 642 - 656. [Abstract] [Full Text] [PDF]
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V. Sorokin, K. Severinov, and M. S. Gelfand Systematic prediction of control proteins and their DNA binding sites Nucleic Acids Res., February 1, 2009; 37(2): 441 - 451. [Abstract] [Full Text] [PDF]
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Y. Lu and S.-H. Sze Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues Nucleic Acids Res., February 1, 2009; 37(2): 463 - 472. [Abstract] [Full Text] [PDF]
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B. L. Schulz and M. Aebi Analysis of Glycosylation Site Occupancy Reveals a Role for Ost3p and Ost6p in Site-specific N-Glycosylation Efficiency Mol. Cell. Proteomics, February 1, 2009; 8(2): 357 - 364. [Abstract] [Full Text] [PDF]
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C. Brochier-Armanet, E. Talla, and S. Gribaldo The Multiple Evolutionary Histories of Dioxygen Reductases: Implications for the Origin and Evolution of Aerobic Respiration Mol. Biol. Evol., February 1, 2009; 26(2): 285 - 297. [Abstract] [Full Text] [PDF]
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C. Chen, T. Ara, and D. Gautheret Using Alu Elements as Polyadenylation Sites: A Case of Retroposon Exaptation Mol. Biol. Evol., February 1, 2009; 26(2): 327 - 334. [Abstract] [Full Text] [PDF]
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B. M. Hallstrom and A. Janke Gnathostome Phylogenomics Utilizing Lungfish EST Sequences Mol. Biol. Evol., February 1, 2009; 26(2): 463 - 471. [Abstract] [Full Text] [PDF]
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D. C. Tully and M. A. Fares Shifts in the Selection-Drift Balance Drive the Evolution and Epidemiology of Foot-and-Mouth Disease Virus J. Virol., January 15, 2009; 83(2): 781 - 790. [Abstract] [Full Text] [PDF]
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Y. Xu, L. Cong, C. Chen, L. Wei, Q. Zhao, X. Xu, Y. Ma, M. Bartlam, and Z. Rao Crystal Structures of Two Coronavirus ADP-Ribose-1''-Monophosphatases and Their Complexes with ADP-Ribose: a Systematic Structural Analysis of the Viral ADRP Domain J. Virol., January 15, 2009; 83(2): 1083 - 1092. [Abstract] [Full Text] [PDF]
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D. J. Heslin, P. Murcia, F. Arnaud, K. Van Doorslaer, M. Palmarini, and J. Lenz A Single Amino Acid Substitution in a Segment of the CA Protein within Gag That Has Similarity to Human Immunodeficiency Virus Type 1 Blocks Infectivity of a Human Endogenous Retrovirus K Provirus in the Human Genome J. Virol., January 15, 2009; 83(2): 1105 - 1114. [Abstract] [Full Text] [PDF]
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