T-COFFEE

T-Coffee is a multiple sequence alignment program. Multiple sequence alignment programs are meant to align a set of sequences previously gathered using other programs such as blast, fasta, sw ...

The main characteristic of T-Coffee is that it will allow you to combine results obtained with several alignment methods. For instance if you have an alignment coming from ClustalW, another alignment coming from Dialign, and a structural alignment of some of your sequences, T-Coffee will combine all that information and produce a new multiple sequence having the best agreement with all these methods.

By default, T-Coffee will compare all your sequences two by two, producing a global alignment and a series of local alignments (using lalign). The program will then combine all these alignments into a multiple alignment.

Installed on the opteron cluster.

Usage version 1.37

• Create a job file which calls t_coffee:

  /biomed/bin/t_coffee sequence-file

  Two output files will be produced: sequence-file.aln, a multiple alignment in a formula similar to ClustalW that can be read by most programs, and sequence-file.dnd, a dendogram in phylip format.

Other documentation

• The T-COFFEE User Guide
• The T-COFFEE home page

See also:

• 3DCoffee: Combining Protein Sequences and Structures within Multiple Sequence Alignments. O. O'Sullivan, K Suhre, C. Abergel, D.G. Higgins, C. Notredame. Journal of Molecular Biology,Vol 340, pp385-395,2004


• T-Coffee: A novel method for multiple sequence alignments. C.Notredame, D. Higgins, J. Heringa,Journal of Molecular Biology,Vol 302, pp205-217,2000


• COFFEE: A New Objective Function For Multiple Sequence Alignmnent. C. Notredame, L. Holme and D.G. Higgins,Bioinformatics,Vol 14 (5) 407-422,1998


• Other sequence analysis software installed at PSC.