Introduction 

    T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Multiple sequence alignment programs are to align a set of sequences previously gathered using other programs such as blast, fasta, etc. T-Coffee allows one to combine results obtained with several alignment methods. If one alignment is from ClustalW and second is from Dialigni, T-Coffee will combine all that information and produce a new multiple sequence having the best alignment from these methods. By default, T-Coffee will compare all your sequences two by two, producing a global alignment and a series of local alignments (using lalign). The program will then combine all these alignments into a multiple alignment.

Here is a useful link to some information on t-coffee: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html

PKGNAME=   t-coffee-1.37

Using T-Coffee: Documentation and tutorials

1 INSTALLATION

A-QUICK INSTALLATION

1. decompress distribution.tar.z
	uncompress distribution.tar.Z

2. untar distribution.tar
	tar -xvf distribution.tar

3. This will create the distribution directory with the following structure:
		distribution/bin
		distribution/doc/t_coffee_doc.ps, t_coffee_doc.pdf, t_coffee_paper.tar in pdf
		
		distribution/t_coffee_source
		distribution/lalign
		distribution/example
		distribution/html

4. Install ClustalW (check before if it is not already installed). You can obtain ClustalW from the EBI Web server (www.ebi.ac.uk) or from the LBM in Strasbourg.

5. Indicate the address and the name of ClustalW on your system:
	-either edit the file define_header.h, in the section PROGRAM PATH
			
#define CLUSTALW_4_TCOFFEE "path/name_of_clustalw"
	
-or set the global variable CLUSTALW_4_TCOFFEE to "path/name_of_clustalw":
			
setenv CLUSTALW_4_TCOFFEE "path/name_of_clustalw"

Note: to be permanent, this last change must be set in your loging file.

6. go into the main directory and type:
	./install

7. add the bin folder to your path, for instance:
set path = ($path . <address of the t_coffee bin folder>) 

Note This must be added to your loging file. An alternative is to move all the binary files into your own bin.


8. Go into example/test and run:

 	t_coffee -in fast_pair test.pep

9. The command 

	diff test.aln reference_test.aln

	These two files must only indicate a difference for the CPU time.

Note: for 8 to work correctly, the new bins must have been added to your
path (Step 5).