T-Coffee is a multiple sequence alignment package. You can use T-Coffee to align sequences or to combine the output of your favorite alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique alignment (M-Coffee).

T-Coffee can align Protein, DNA and RNA sequences. It is also able to combine sequence information with protein structural information (3D-Coffee/Expresso), profile information (PSI-Coffee) or RNA secondary structures (R-Coffee).

This presentation gives an overview of the T-Coffee algorithm and of the original implementation and validatation of the package. The full list of associated papers is available on the following links: algorithms and servers. The original T-Coffee paper is:

T-Coffee: A novel method for multiple sequence alignments.
Notredame,Higgins,Heringa,JMB,302(205-217)2000 [pdf][medline]

• www.tcoffee.org
• CRG
• SIB
• CNRS
• EBI

• Q: What is the most accurate mode?

  A: for proteins, try t_coffee yourseq -mode accurate. For RNA, try: t_coffee -mode rcoffee.

• Q: What is the meaning of the color coded html output?

  A: Red bits are very reliable, while green and blue bits are unreliable. This color scheme is named the TCS index and it uses the consistency among pairwise alignments for this estimationto estimate reliability. An extensive validation of the TCS is available from the original MBE paper and more details are given on the TCS homepage. Online evaluations can be carried out on the TCS server.

• Q: Which mode should I use on www.tcoffee.org server 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. The most accurate mode (-mode=accurate) is now available at this T-Coffee web server mirror

• 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 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 (and slightly less accurate):

  t_coffee  your_seq.pep -mode 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 -profile aln1 aln2 aln3

• Q: What is the meaning of the name "T-Coffee" ?

  A: T-Coffee stands for Tree based Consistency Objective Function For AlignmEnt Evaluation.

T-Coffee relies on your feeback. Please send me an Email if you wish to make a request, a comment, or report a bug!

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Dr. Cedric Notredame, PhD.
Group Leader
Comparative Bioinformatics Group
Bioinformatics and Genomics Programme
Center for Genomic Regulation (CRG)
Dr Aiguader, 88
08003 Barcelona
Spain
Email: cedric.notredame@gmail.com
HOME : http://www.tcoffee.org/index.html
GROUP: CRG
Phone: +34 933 160 271
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