A Meta-Multiple Sequence Alignment Tool


What is M-Coffee?

M-Coffee is a multiple sequence alignment Package. It is part of the T-Coffee distribution. The specificity of M-Coffee is that rather than computing a multiple sequence alignment on its own, it uses other packages to compute the alignments. It then uses T-Coffee to combine all these alignents into one unique final alignment. In practice, this means that if you are using several packages to generate your alignments, you can comine these alignments rather tna chooding one of them. In practice we have shown that the combined alignments are on average better than the initila alignments. Furthermore, the regions where they agree tend to be correctly aligned.

A list of related publications is available here and the following presentation provides an overview of the algorithm and its validation.



  • M-Coffee is only a special mode of T-Coffee. Download the latest T-Coffee version here.


1-Follow the standard T-Coffee installation procedure.

2-Install all the multiple sequence alignment packages you want to combine. A list of these packages and their download address is available here. You should also take a look at the T-Coffee Technical Documentation. The latest list of packages interfaced with T-Coffee can also be obtained with the simple intruction t_coffee > package_list

Warning! Some packages, like Dialign or POA, require specific files to be available. Whenever this happens, you should copy every required file in the ~/.tcoffee/mcoffee directory that was created by the installation procedure.


Given a sequence file foo.pep M-Coffee outputs a file named foo.html that contains a color coded indication of the agreement between all the combined methods. Red brick regions are in perfect agreement across all the methods, while blue regions have a very poor agreement. Red brick regions can safely be assumed to be correct while blue regions should be discarted. Green and Yellow regions should also be used with caution, especially when reconstructing a tree or building a profile. The top of the output provides the average conistency (0-100) for each sequence, thus indicating wether some sequences may have a less reliable alignment. A score lower than 50 should be considered poor.


The full documentation is on the T-Coffee Homepage. But the following shortcuts may be useful.

To run all the available methods, type
t_coffee foo.seq -mode mcoffee
To only run the methods you are interested in (these methods must be installed on your system), type:
t_coffee foo.seq -method proba_msa muscle_msa mafft_msa


  • MSA Mehods Available for combination within M-Coffee


    Our projects relie on your feeback. Please send me an E-mail 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
    Email: cedric.notredame@europe.com
    HOME : http://www.tcoffee.org/
    Phone: +34 933 160 271