MUSCLE: Multiple sequence alignment with improved accuracy and speed

Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004

Volumn , Issue , 2004, Pages 728-729

  Edgar, Robert C ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BENCHMARKS; BINARY TREE; MULTIPLE SEQUENCE ALIGNMENT (MSA) ALGORITHMS; PROTEIN SEQUENCES;

ALGORITHMS; COMPUTATIONAL COMPLEXITY; DATABASE SYSTEMS; MATRIX ALGEBRA; PROTEINS; TREES (MATHEMATICS);

COMPUTER SOFTWARE;

EID: 14044274276     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (14)

1. C. Notredame, "Recent progress in multiple sequence alignment: a survey," Pharmacogenomics, vol. 3, pp. 131-44, 2002.
2. R. C. Edgar, "MUSCLE: multiple sequence alignment with high accuracy and high throughput," Nucleic Acids Res, vol. 32, pp. 1792-1797, 2004.
3. C. Notredame, D. G. Higgins, and J. Heringa, "T-Coffee: A novel method for fast and accurate multiple sequence alignment," J Mol Biol, vol. 302, pp. 205-17, 2000.
4. R. C. Edgar, "Local homology recognition and distance measures in linear time using compressed amino acid alphabets," Nucleic Acids Res, vol. 32, pp. 380-5, 2004.
5. P. H. A. Sneath and R. R. Sokal, Numerical taxonomy. San Francisco: Freeman, 1973.
6. D. F. Feng and R. F. Doolittle, "Progressive sequence alignment as a prerequisite to correct phylogenetic trees," J Mol Evol, vol. 25, pp. 351-60, 1987.
7. P. Hogeweg and B. Hesper, "The alignment of sets of sequences and the construction of phyletic trees: an integrated method," J Mol Evol, vol. 20, pp. 175-86, 1984.
8. R. C. Edgar, "Multiple sequence alignment with reduced time and space complexity," (Submitted), 2004.
9. M. Kimura, The neutral theory of molecular evolution: Cambridge University Press, 1983.
10. M. Hirosawa, Y. Totoki, M. Hoshida, and M. Ishikawa, "Comprehensive study on iterative algorithms of multiple sequence alignment," Comput Appl Biosci, vol. 11, pp. 13-8, 1995.
11. A. Bahr, J. D. Thompson, J. C. Thierry, and O. Poch, "BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations," Nucleic Acids Res, vol. 29, pp. 323-6, 2001.
12. I. Van Walle, I. Lasters, and L. Wyns, "Align-m-a new algorithm for multiple alignment of highly divergent sequences," Bioinformatics, 2004.
13. C. P. Ponting, J. Schultz, F. Milpetz, and P. Bork, "SMART: identification and annotation of domains from signalling and extracellular protein sequences," Nucleic Acids Res, vol. 27, pp. 229-32, 1999.
14. J. D. Thompson, D. G. Higgins, and T. J. Gibson, "CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice," Nucleic Acids Res, vol. 22, pp. 4673-80, 1994.