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T-Coffee [1] is a Multiple Sequence Alignment tool which is available here. Additional work incorporating 3D Structures into the alignment process has been added to T-Coffee as well [2, 3].


  1. Notredame C, Higgins DG, and Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. 2000 Sep 8;302(1):205-17. DOI:10.1006/jmbi.2000.4042 | PubMed ID:10964570 | HubMed [tcoffee]
  2. Poirot O, Suhre K, Abergel C, O'Toole E, and Notredame C. 3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W37-40. DOI:10.1093/nar/gkh382 | PubMed ID:15215345 | HubMed [poirot]
  3. O'Sullivan O, Suhre K, Abergel C, Higgins DG, and Notredame C. 3DCoffee: combining protein sequences and structures within multiple sequence alignments. J Mol Biol. 2004 Jul 2;340(2):385-95. DOI:10.1016/j.jmb.2004.04.058 | PubMed ID:15201059 | HubMed [osullivan]
  4. Poirot O, O'Toole E, and Notredame C. Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments. Nucleic Acids Res. 2003 Jul 1;31(13):3503-6. PubMed ID:12824354 | HubMed [poirot03]
  5. Notredame C. Recent progress in multiple sequence alignment: a survey. Pharmacogenomics. 2002 Jan;3(1):131-44. DOI:10.1517/14622416.3.1.131 | PubMed ID:11966409 | HubMed [notredame_review]
  6. Notredame C. Mocca: semi-automatic method for domain hunting. Bioinformatics. 2001 Apr;17(4):373-4. PubMed ID:11301309 | HubMed [mocca]
  7. Notredame C, Holm L, and Higgins DG. COFFEE: an objective function for multiple sequence alignments. Bioinformatics. 1998 Jun;14(5):407-22. PubMed ID:9682054 | HubMed [coffee]
All Medline abstracts: PubMed | HubMed
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