T-Coffee

From BioPerl

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].

References

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 pmid:10964570. PubMed 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 pmid:15215345. PubMed 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 pmid:15201059. PubMed 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. pmid:12824354. PubMed 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 pmid:11966409. PubMed HubMed [notredame_review]
6. Notredame C. Mocca: semi-automatic method for domain hunting. Bioinformatics 2001 Apr; 17(4) 373-4. pmid:11301309. PubMed 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. pmid:9682054. PubMed HubMed [coffee]

All Medline abstracts: PubMed HubMed