T-Coffee is a rather new multiple sequence alignment package based on consistency indices between pairwise local and global sequence alignments and the final multiple sequence alignment.  It can also combine and/or evaluate other methods and alignments based on these indices.  It is available on all HPC nodes as a part of the Rocks Bio Roll.

Using T-Coffee on HPC

T-Coffee is available on all HPC nodes as a part of the Rocks Bio Roll.  Documentation is available in the Bio Roll and in /opt/Bio/t_coffee/doc/; more extensive instructions and a tutorial is available through the T-Coffee Home Page.  Furthermore, I have a soon to be published by Humana Press manuscript that introduces the concepts of all multiple sequence alignment, and then explores T-Coffee in more depth.  See all of the program options with:

t_coffee -help

Auxillary alignment programs, data files, and the necessary environment variable to allow T-Coffee's M-Coffee 'meta' mode to work have also been added to the HPC.  At this point the structural components that allow T-Coffee to do structure-based, 3D-Coffee, alignment have not been installed.

T-Coffee can also be run through the SeaView editor as an "external method."