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 aligment
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 amultiple alignment.