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.
