MUSCLE: multiple sequence alignment with high accuracy and high throughput

Nucleic Acids Research
Robert C Edgar

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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Dec 16, 2011·Proceedings of the National Academy of Sciences of the United States of America·Xiangshu JinLawrence Shapiro
May 24, 2012·Proceedings of the National Academy of Sciences of the United States of America·Thomas LavstsenThor G Theander
Mar 1, 2012·Proceedings of the National Academy of Sciences of the United States of America·Ricardo AcuñaJocelyn K C Rose
Jun 13, 2012·Proceedings of the National Academy of Sciences of the United States of America·Joseph L RobertsDavid L Wiest
Jul 4, 2012·Proceedings of the National Academy of Sciences of the United States of America·Paul K FyfeWilliam N Hunter
Oct 9, 2012·Proceedings of the National Academy of Sciences of the United States of America·Gergely J SzöllosiVincent Daubin
Jan 2, 2013·Proceedings of the National Academy of Sciences of the United States of America·Ali Morton WalshDavid L Adelson
Jun 12, 2012·Proceedings of the National Academy of Sciences of the United States of America·Joanna I SułkowskaAndrzej Stasiak
Nov 16, 2012·Proceedings of the National Academy of Sciences of the United States of America·Victoria L HewittTrevor Lithgow
Jul 25, 2012·Proceedings of the National Academy of Sciences of the United States of America·Paula V Welander, Roger E Summons
Oct 17, 2012·Proceedings of the National Academy of Sciences of the United States of America·Christelle DesnuesDidier Raoult
Nov 28, 2012·Proceedings of the National Academy of Sciences of the United States of America·Emmanuel D LevySarah A Teichmann
Jul 28, 2012·Proceedings of the National Academy of Sciences of the United States of America·Naupaka B Zimmerman, Peter M Vitousek
Jan 16, 2013·Proceedings of the National Academy of Sciences of the United States of America·Bettina E SchirrmeisterHomayoun C Bagheri
Sep 6, 2012·Proceedings of the National Academy of Sciences of the United States of America·Randy B StockbridgeChristopher Miller
Dec 19, 2012·Proceedings of the National Academy of Sciences of the United States of America·Wannes DermauwThomas Van Leeuwen
Jan 9, 2013·Proceedings of the National Academy of Sciences of the United States of America·Heidi H LuotoAnssi M Malinen
Feb 6, 2013·Proceedings of the National Academy of Sciences of the United States of America·Chungoo ParkJianzhi Zhang
Mar 20, 2013·Proceedings of the National Academy of Sciences of the United States of America·Sanjay ChandrianiAmy L Kistler
Mar 27, 2013·Proceedings of the National Academy of Sciences of the United States of America·Dana YaffeShimon Schuldiner
Mar 15, 2013·Proceedings of the National Academy of Sciences of the United States of America·Linda FoitJames C A Bardwell
May 16, 2013·Proceedings of the National Academy of Sciences of the United States of America·Marc W Cadotte
Jul 13, 2013·Proceedings of the National Academy of Sciences of the United States of America·Joseph J CarterDenise A Galloway
May 3, 2013·Proceedings of the National Academy of Sciences of the United States of America·Franck PrugnolleFrançois Renaud
Sep 21, 2013·Proceedings of the National Academy of Sciences of the United States of America·Andrian GutuDavid M Kehoe
Jul 10, 2013·Proceedings of the National Academy of Sciences of the United States of America·So NakagawaMartha L Bulyk
Nov 28, 2013·Proceedings of the National Academy of Sciences of the United States of America·Georgy SmyshlyaevOlga Novikova
Oct 9, 2013·Proceedings of the National Academy of Sciences of the United States of America·Juliane SchaerKai Matuschewski
Nov 28, 2013·Proceedings of the National Academy of Sciences of the United States of America·Alexander HaywardPatric Jern
May 15, 2009·The Journal of Biological Chemistry·Mario Sandoval-CalderónChristian Sohlenkamp
Aug 4, 2009·The Journal of Biological Chemistry·Sayanti SahaSandhya S Visweswariah
Aug 14, 2009·The Journal of Biological Chemistry·James R R Whittle, Thomas U Schwartz
Feb 9, 2010·The Journal of Biological Chemistry·Marc F LensinkJean-Marie Ruysschaert
Apr 9, 2010·The Journal of Biological Chemistry·Béatrice Clouet-d'OrvalAgamemnon J Carpousis
May 18, 2010·The Journal of Biological Chemistry·Antonio J Martín-GalianoJosé M Andreu
Sep 28, 2010·The Journal of Biological Chemistry·Christopher S CrowleyTodd O Yeates
Nov 5, 2010·The Journal of Biological Chemistry·Kristina FaxénJesper Vuust Møller
Oct 30, 2010·The Journal of Biological Chemistry·Min-Hyung RyuMark Gomelsky
Jan 26, 2011·The Journal of Biological Chemistry·Immo A HansenAlexander S Raikhel
Dec 21, 2010·The Journal of Biological Chemistry·Pierre V MaillardDidier Trono
Feb 23, 2011·The Journal of Biological Chemistry·Christopher R RiveraR Dyche Mullins
Feb 19, 2011·The Journal of Biological Chemistry·Antionette L WilliamsEdward L Stuenkel
May 14, 2011·The Journal of Biological Chemistry·Karl E ZahnSylvie Doublié
Nov 15, 2011·The Journal of Biological Chemistry·Ivana L ViolaDaniel H Gonzalez
Dec 17, 2011·The Journal of Biological Chemistry·Alicia R Timme-LaragyMark E Hahn
Sep 23, 2011·The Journal of Biological Chemistry·Dominique ColinetMarylène Poirié
Jan 5, 2012·The Journal of Biological Chemistry·Melanie DochowRichard K Plemper
May 31, 2012·The Journal of Biological Chemistry·Zhiwei ChenSwapnil R Chhabra
Apr 27, 2012·The Journal of Biological Chemistry·Daniel LundinMartin Högbom
Sep 11, 2012·The Journal of Biological Chemistry·Michael T GrispoJay F Storz
Sep 21, 2012·The Journal of Biological Chemistry·Dara ForouzanAndrei N Lupas
Oct 5, 2012·The Journal of Biological Chemistry·Riad SeddikBernhard Bettler
Sep 5, 2008·The Journal of Biological Chemistry·Shiho KawamuraThomas B Kornberg
Dec 17, 2008·The Journal of Biological Chemistry·Benjamin ChagotWalter J Chazin
Jan 17, 2009·The Journal of Biological Chemistry·Johannes StuttmannLaurent D Noël
Apr 15, 2009·The Journal of Biological Chemistry·Chih-chin HuangJohn J G Tesmer
Mar 21, 2008·Molecular & Cellular Proteomics : MCP·Yu QuanTao Tao
Nov 26, 2009·Avian Pathology : Journal of the W.V.P.A·James F X WellehanScott P Terrell
Jun 15, 2010·Avian Pathology : Journal of the W.V.P.A·Dana GoldenbergJacob Pitcovski
Feb 19, 2011·Avian Pathology : Journal of the W.V.P.A·Róbert GlávitsAdám Dán
Jun 15, 2012·Journal of Biomolecular Structure & Dynamics·Jun Cao, Feng Shi
Jul 27, 2012·Journal of Biomolecular Structure & Dynamics·Alessia RuggieroRita Berisio
Mar 4, 2006·SAR and QSAR in Environmental Research·A J M Carpy, N Marchand-Geneste
Mar 31, 2009·AIDS Research and Human Retroviruses·Mattia C F ProsperiMaurizio Zazzi
Nov 20, 2010·AIDS Research and Human Retroviruses·Joana Paixao Monteiro-CunhaLuiz Carlos Junior Alcantara
Sep 16, 2011·AIDS Research and Human Retroviruses·Allison K DelongRami Kantor
May 27, 2008·Antioxidants & Redox Signaling·Silvio C E TosattoMatilde Maiorino