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.
To run this software interactively in a Linux environment run the command:
module load t-coffee t_coffee -in fast_pair test.pep