Information about software packages installed on the ICHEC systems.
T-Coffee is a multiple sequence alignment package. You can use T-Coffee to align sequences or to combine the output of your favorite alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique alignment (M-Coffee).
T-Coffee can align protein, DNA and RNA sequences. It is also able to combine sequence information with protein structural information (3D-Coffee/Expresso), profile information (PSI-Coffee) or RNA secondary structures (R-Coffee).
T-Coffee is a freeware opensource package distributed under the GNU public license.
To use T-Coffee load the relevant environment module:
Further information can be obtained from http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html.
How to cite T-Coffee:
Notredame C., Higgins D.G. and Heringa J. (2000)
T-Coffee: A novel method for fast and accurate multiple sequence alignment.
Journal of Molecular Biology 302(1): 205-217.