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T-Coffee: A novel method for fast and accurate multiple sequence alignment.
Notredame C, Higgins DG, Heringa J. Notredame C, et al. J Mol Biol. 2000 Sep 8;302(1):205-17. doi: 10.1006/jmbi.2000.4042. J Mol Biol. 2000. PMID: 10964570
SAGA: sequence alignment by genetic algorithm.
Notredame C, Higgins DG. Notredame C, et al. Nucleic Acids Res. 1996 Apr 15;24(8):1515-24. doi: 10.1093/nar/24.8.1515. Nucleic Acids Res. 1996. PMID: 8628686 Free PMC article.
RAGA: RNA sequence alignment by genetic algorithm.
Notredame C, O'Brien EA, Higgins DG. Notredame C, et al. Nucleic Acids Res. 1997 Nov 15;25(22):4570-80. doi: 10.1093/nar/25.22.4570. Nucleic Acids Res. 1997. PMID: 9358168 Free PMC article.
COFFEE: an objective function for multiple sequence alignments.
Notredame C, Holm L, Higgins DG. Notredame C, et al. Bioinformatics. 1998 Jun;14(5):407-22. doi: 10.1093/bioinformatics/14.5.407. Bioinformatics. 1998. PMID: 9682054
A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3.
Dietmann S, Park J, Notredame C, Heger A, Lappe M, Holm L. Dietmann S, et al. Among authors: notredame c. Nucleic Acids Res. 2001 Jan 1;29(1):55-7. doi: 10.1093/nar/29.1.55. Nucleic Acids Res. 2001. PMID: 11125048 Free PMC article.
Recent progress in multiple sequence alignment: a survey.
Notredame C. Notredame C. Pharmacogenomics. 2002 Jan;3(1):131-44. doi: 10.1517/14622416.3.1.131. Pharmacogenomics. 2002. PMID: 11966409 Review.
APDB: a novel measure for benchmarking sequence alignment methods without reference alignments.
O'Sullivan O, Zehnder M, Higgins D, Bucher P, Grosdidier A, Notredame C. O'Sullivan O, et al. Among authors: notredame c. Bioinformatics. 2003;19 Suppl 1:i215-21. doi: 10.1093/bioinformatics/btg1029. Bioinformatics. 2003. PMID: 12855461
3DCoffee: combining protein sequences and structures within multiple sequence alignments.
O'Sullivan O, Suhre K, Abergel C, Higgins DG, Notredame C. O'Sullivan O, et al. Among authors: notredame c. J Mol Biol. 2004 Jul 2;340(2):385-95. doi: 10.1016/j.jmb.2004.04.058. J Mol Biol. 2004. PMID: 15201059
3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment.
Poirot O, Suhre K, Abergel C, O'Toole E, Notredame C. Poirot O, et al. Among authors: notredame c. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W37-40. doi: 10.1093/nar/gkh382. Nucleic Acids Res. 2004. PMID: 15215345 Free PMC article.
M-Coffee: combining multiple sequence alignment methods with T-Coffee.
Wallace IM, O'Sullivan O, Higgins DG, Notredame C. Wallace IM, et al. Among authors: notredame c. Nucleic Acids Res. 2006 Mar 23;34(6):1692-9. doi: 10.1093/nar/gkl091. Print 2006. Nucleic Acids Res. 2006. PMID: 16556910 Free PMC article.
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