T-COFFEE for Debian ------------------- T-COFFEE comes with a special mode, M-COFFEE, that makes it possible to combine the output of many multiple sequence alignment packages. In its published version, it uses MUSCLE, PROBCONS, POA, DiAlign-T, MAFFT, Clustal W, PCMA and T-Coffee. A special version has been made for Debian, DM-Coffee, that uses only free software by replacing Clustal W by Kalign. Using the 8 Methods of M-Coffee can sometimes be a bit heavy. You can use a subset of your favorite methods if you prefer. This version of T-COFFEE has been patched to use the latest program of the DiAlign family, DiAlign-TX. To install all the necessary programs for running DM-COFFEE, you can run use the option `~Rsuggests:^package$' of the `aptitude' package manager, or the command `apt-get -o APT::Install-Suggests=true install'. In order to download clustalw for M-COFFEE, please add the non-free section in the file /etc/apt/sources.list (it has a man page). Whenever appropriate please cite this software as 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 and/or T-Coffee: A novel method for multiple sequence alignments. C.Notredame, D. Higgins, J. Heringa, Journal of Molecular Biology,Vol 302, pp205-217, 2000 and/or COFFEE: A New Objective Function For Multiple Sequence Alignmnent. C. Notredame, L. Holme and D.G. Higgins, Bioinformatics, Vol 14 (5) 407-422, 1998 and/or M-Coffee: combining multiple sequence alignment methods with T-Coffee. Wallace IM, O'Sullivan O, Higgins DG, Notredame C. Nucleic Acids Res. 2006 Mar 23;34(6):1692-9.