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T-Coffee
Multiple Sequence Alignment Tools |
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What is T-Coffee?
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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]
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T-Coffee is a freeware opensource package distributed under the GNU public license
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| T-Coffee runs on UNIX and UNIX-like platforms (Linux, cygwin and MacOSX). Download the latest version (recommended) or download one of the available binaries. |
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| Latest Version: |
Version_7.97 |
| Binaries : |
[Binaries] |
| Previous Versions: |
[Archives] |
| Older Versions: |
cedric.notredame@europe.com |
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UNIX/LINUX/Mac OSX |
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T-Coffee requires gcc, g77, makefile, CPAN, an internet connection and your root password |
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Download and save the Packagegunzip t_coffee.tar.gztar -xvf t_coffee.tarcd T-COFFEE_distribution_Version_7.97./install
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| This installation procedure is semi-interactive. It will prompt questions here and there. You can interrupt it any time and resume it later. |
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| The install procedure carries out three distinct tasks: Compilation of T-Coffee (C program), Compilation and Installation of SOAP::Lite (Perl Module), Download/Compilation and Installation of all the T-Coffee companion packages required for all possible T-Coffee flavors (tcoffee,expresso,3dcoffee,mcoffee,rcoffee). Except for T-Coffee, the installer will only install the packages that are NOT already on your computer. If you want a lighter or more specific installation, you can try any of the following: |
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./install tcoffee
./install rcoffee
./install expresso
./install 3dcoffee
./install mcoffee
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| While Installing SOAP::Lite, CPAN will ask you many questions: say Yes to all or type return to keep the default values. If everything went well, the procedure has created in the bin directory two executables: t_coffee and TMalign (Make sure these executables are on your $PATH!). |
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| If you have not managed to install SOAP::Lite, you can re-install it anytime (from anywhere) using steps 1-2 |
| If you cannot log as root, or if for some reason this procedure does not work, see with your system manager and/or go directly to the CPAN repository of SOAP::Lite. You will still be able to use the most basic functions of T-Coffee. |
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IMPORTANT: The purpose of SOAP::Lite is to allow T-Coffee the use of the EBI webservices such as webblast. BLAST brings many functionalities to T-Coffee and if you cannot install SOAP we suggest you go to the Installing BLAST for T-Coffee section of the Technical Doumentation (in the Installation section). There you will find alternative ways of using BLAST without SOAP. It is also in this document that you will find all the information required for a full installation of T-Coffee |
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Microsoft Windows/Cygwin |
| Install Cygwin |
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- Download The Installer (NOT Cygwin/X)
- Click on view to list ALL the packages
- Select: gcc-core, make, wget
- Optional: ssh, xemacs, nano
- Run mkpasswd in Cywin (as requested when you start cygwin)
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| Install T-Coffee within Cygwin using the Unix procedure |
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| mode |
Fast |
t_coffee foo.seq |
| Seq. |
All |
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| Accuracy |
Medium |
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| mode |
Accurate |
t_coffee foo.seq -mode accurate |
| Seq. |
Proteins |
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| Accuracy |
High but slow |
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| mode |
R-Coffee |
t_coffee foo.seq -mode rcoffee |
| Seq. |
RNA |
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| Accuracy |
High |
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| mode |
Very Fast |
t_coffee foo.seq -mode quickaln |
| Seq. |
All |
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| Accuracy |
Medium Low |
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| mode |
Low Mem. |
t_coffee foo.seq -mode memory |
| Seq. |
RNA |
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| Accuracy |
Medium |
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| mode |
Expresso |
t_coffee foo.seq -mode expresso |
| Seq. |
All |
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| Accuracy |
High |
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| mode |
M-Coffee |
t_coffee foo.seq -mode mcoffee |
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All |
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| Accuracy |
Medium High |
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Q: What is the most accurate mode?
A: for proteins, try t_coffee yourseq -mode accurate. For RNA, try: t_coffee -mode rcoffee.
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. The most accurate mode (-mode=accurate) is not yet available via a web server
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.
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T-Coffee relies on your feeback. Please send me an
Email if you wish to make a request, a comment, or report a bug!
*******************************************
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@europe.com
HOME : http://www.tcoffee.org/homepage.html
GROUP: CRG
Phone: +34 933 160 271
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