T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Version 2.00 and higher can combine sequences and structures.
T-Coffee comes in different flavors. 3D-Coffee makes it possible to combine the alignment of sequences and structures. M-Coffee makes it possible to combine the output of several multiple sequence alignment packages. R-Coffee makes it possible to align multiple RNA sequences using their predicted secondary structures. All these various modes are available on the web server and are included in the main distribution.
T-Coffee makes it possible to combine of a collection of multiple/pairwise, global/local alignments into a single one. Your alignments may come from any source. T-Coffee also makes it possible to estimate the level of consistency of each position within the new alignment with the rest of the alignments. This consistency is usualy an indicator of alignment accuracy.
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[pdf]
T-Coffee: A novel method for multiple sequence alignments.
C.Notredame, D. Higgins, J. Heringa,Journal of Molecular Biology,Vol 302,
pp205-217,2000[pdf]
COFFEE: A New Objective Function For Multiple Sequence Alignmnent.
C. Notredame, L. Holme and D.G. Higgins,Bioinformatics,Vol 14 (5)
407-422,1998[pdf]
Simplest usage: t_coffee sequence_file
The color scheme of T-Coffee is an indicator of the reliability of the alignment. Red bits are the more consistent and therefore the more likely to be correctly aligned. Blue bits are the less trustable. More information of that scoring scheme can be found in the following book chapter [pdf]. Please cite: Notredame, C. and C. Abergel, Using Multiple Alignment Methods to Assess the Quality of Genomic Data Analysis, in Bioinformatics and Genomes: Current Perspectives, M. Andrade, Editor. 2003, Horizon Scientific Press. p. 30-50.
T-Coffee is an open source freeware. Its purpose is to help combining the output of alternative alignment methods. We will do everything we can to encourage and support the inclusion of T-Coffee in third party packages. Whenever you do so, please contact us and send us an example of the way you use T-Coffee. We will then insure that future releases remain compatible with your package.
We currently support:
We have tried to set up a complete FAQ in the DOC, yet, here is a selection my VFAQ
Q: What is the meaning of the name "T-Coffee" ?
A: T-Coffee stands for Tree based Consistency Objective Function For AlignmEnt Evaluation.
Q: Which Server should I use on www.tcoffee.org to get the best alignment ?
A: If you have proteins, expresso is likely to be the most accurate flavor, as it uses potential known 3D-Structures similar to your sequences. Otherwise, our benchmarks indicate that M-Coffee is the next best alternative. M-Coffee runs most known Multiple Sequence Alignment methods and combines them into one final alignment.
Q: What is the Color Code ?
A:The color scheme of T-Coffee is an indicator of the reliability of the alignment. Red bits are the more consistent and therefore the more likely to be correctly aligned. Blue bits are the less trustable. More information of that scoring scheme can be found in the following book chapter [pdf]. Please cite: Notredame, C. and C. Abergel, Using Multiple Alignment Methods to Assess the Quality of Genomic Data Analysis, in Bioinformatics and Genomes: Current Perspectives, M. Andrade, Editor. 2003, Horizon Scientific Press. p. 30-50.
Q: Which Paper Shall I cite ?
A: It is very important you cite us if you use our ressources. We depend on it for funding! If you use the local version of T-Coffee, cite the original 2000 paper (cf above). Otherwise, cite the paper that corresponding to the server you have been using (click on the "cite" button associated with every server on www.tcoffee.org).
Q: What to do if I run out of memory ? (I)
A: Here is the less memory hungry mode of t_coffee:
t_coffee your_seq.pep -special_mode low_memory
Q: What to do if I still run out of memory ? (II)
A: Divide your sequences in subgroups, align them individually and use
t_coffee -in slow_pair lalign_id_pair -profile aln1 aln2 aln3
It is possible to integrate T-Coffee in seaview the sequence edition package of Manolo Gouy. Seaview allows you to visualize, edit and realign sequences within a set.
If you wish to create a t_coffee server, please inform me, and I will link your server to this page. I will be happy to provide you with all the necessary informations. The T-Coffee distribution contains an HTML page and a Perl script that can be adapted to create your own server. Check the html directory in the distribution.
Currently Available T_coffee servers:
A great thanks to the following people who contribute to T-Coffee by reporting Bugs/Problems and proposing new solutions.
T-Coffee is a new method and feed back is very important. Please send me an Email if you wish to make a request or a comment cedric.notredame@europe.com