T-coffee - Multiple Sequence Alignment Program

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T-Coffee is a versatile tool for making multiple sequence alignments. Its aim is to combine heterogeneous sources of information. The current implementation has been especially designed for combining local and global alignments, respectively from ClustalW and Lalign. It can also be used to combine a series of alternative multiple sequence alignments of the same sequences.

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To run this software interactively in a Linux environment run the command:

module load t-coffee
t_coffee -in fast_pair test.pep

Setting Up Your Environment

You must initialize your environment including default paths and environmental variables which the package uses to access the programs and associated files. To do this, enter the following command:
module load bioinformatics

If you access this package on a regular basis, you can add this line to your ~/.cshrc file so that your environment will be initialized for T-Coffee every time you log in.



  # initialize and load modules

  if( -e /usr/local/share/modules/init/tcsh ) then

     unsetenv PATH MANPATH

     source /usr/local/share/modules/init/tcsh

     module load base

     module load bioinformatics



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