MUSCLE swMATH ID: 13193 Software Authors: R.C. Edgar Description: 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. Homepage: http://nar.oxfordjournals.org/content/32/5/1792.short Related Software: ClustalW; MAFFT; T-coffee; BLAST; PSI-BLAST; DIALIGN; ProbCons; Kalign; Clustal X; Balibase; UniProt; CLUSTAL; Probalign; R; Pfam; DIALIGN-TX; MrBayes; SABmark; MUMMALS; LAGAN Cited in: 51 Documents all top 5 Cited by 152 Authors 2 Amani, Jafar 2 Boys, Richard J. 2 Daskalakis, Constantinos 2 Embley, T. Martin 2 Fattahian, Yaser 2 Gançarski, Pierre 2 Gargari, Seyed Latif Mousavi 2 Heaps, Sarah E. 2 Nye, Tom M. W. 2 Petitjean, François 2 Rahbar, Mohammad Reza 2 Rasooli, Iraj 2 Roch, Sébastien 2 Williams, Tom A. 1 Alanis-Lobato, Gregorio 1 Althaus, Ernst 1 Amiri, Saeid 1 Andoni, Alexandr 1 Andrade-Navarro, Miguel A. 1 Arribas-Gil, Ana 1 Axelson-Fisk, Marina 1 Baranwal, Manoj 1 Becerra, Arturo 1 Berkemer, Sarah J. 1 Brochier-Armanet, Céline 1 Bunnik, Evelien M. 1 Canzar, Stefan 1 Carugo, Oliviero 1 Chadsuthi, Sudarat 1 Chen, Guang-Wu 1 Chen, Jingan 1 Chen, Weiyang 1 Cherlin, Svetlana 1 Chi, Zhongxian 1 Clarke, Bertrand S. 1 Clarke, Jennifer Lynn 1 Dabba, Ali 1 Dahl, David B. 1 Daugelaite, Jurate 1 Davidson, Ruth 1 Day, Ryan 1 de Farias, Sávio Torres 1 DeBlasio, Dan 1 Delaye, Luis 1 Desai, Dhwani K. 1 Drellich, Elizabeth 1 Du, Zhihua 1 Duan, Victor 1 Durden, Chris 1 Ebrahimi, Samaneh 1 Eisenhaber, Frank 1 Fan, Xiaodan 1 Fang, Weiwu 1 Federico, Maria 1 Gainer-Dewar, Andrew 1 Girimurugan, Senthil Balaji 1 Gong, Yu-Nong 1 Gronau, Ilan 1 Guénoche, Alain 1 Guo, Xuan 1 Guyon, Frédéric 1 Harrington, Heather A. 1 Hasan, Md. Abid 1 Hassidim, Avinatan 1 He, Qijun 1 Heckel, Reinhard 1 Heitsch, Christine E. 1 Hernández-Morales, Ricardo 1 Höner zu Siederdissen, Christian 1 Hosseininasab, Amin 1 Huang, Hsin-Hsiung 1 Huang, Zunnan 1 Iliopoulos, Costas S. 1 Jahangiri, Abolfazl 1 Jain, Sahil 1 Jalali, Marziyeh 1 Jiménez-Corona, María Eugenia 1 José, Marco V. 1 Kececioglu, John D. 1 Keith, Jonathan M. 1 Ketterlin, Alain 1 Lárraga-Ramírez, María E. 1 Lazcano, Antonio 1 Le Roch, Karine 1 Lennox, Kristin P. 1 Li, Weiwei 1 Liao, Bo 1 Lin, Feng 1 Lin, Hao 1 Liu, Jun S. 1 Liu, Yong 1 Lonardi, Stefano 1 Lynn, Andrew M. 1 Matias, Catherine 1 Mier, Pablo 1 Minin, Vladimir N. 1 Modchang, Charin 1 Mora-Gutiérrez, Roman Anselmo 1 Moran, Shlomo 1 Nandi, Soumyadeep ...and 52 more Authors all top 5 Cited in 29 Serials 10 Journal of Theoretical Biology 4 Computational Biology and Chemistry 3 Statistical Applications in Genetics and Molecular Biology 2 Computational Biology 2 Methods in Molecular Biology 1 Discrete Applied Mathematics 1 Information Processing Letters 1 Bulletin of Mathematical Biology 1 Biometrics 1 Computing 1 Theoretical Computer Science 1 Statistical Science 1 Algorithmica 1 The Annals of Applied Probability 1 Pattern Recognition 1 Stochastic Processes and their Applications 1 INFORMS Journal on Computing 1 Journal of Combinatorial Optimization 1 Data Mining and Knowledge Discovery 1 Statistical Modelling 1 Mathematics in Computer Science 1 Advances in Data Analysis and Classification. ADAC 1 Computational & Mathematical Methods in Medicine 1 The Annals of Applied Statistics 1 Foundations and Trends in Communications and Information Theory 1 1 Journal of Computational and Graphical Statistics 1 ISRN Biomathematics 1 INFOR: Information Systems and Operational Research all top 5 Cited in 13 Fields 40 Biology and other natural sciences (92-XX) 13 Statistics (62-XX) 10 Computer science (68-XX) 6 Operations research, mathematical programming (90-XX) 4 Probability theory and stochastic processes (60-XX) 3 Combinatorics (05-XX) 3 Numerical analysis (65-XX) 1 General and overarching topics; collections (00-XX) 1 History and biography (01-XX) 1 Algebraic geometry (14-XX) 1 Linear and multilinear algebra; matrix theory (15-XX) 1 Functional analysis (46-XX) 1 Information and communication theory, circuits (94-XX) Citations by Year