T-Coffee is a multiple sequence alignment program. Multiple sequence alignment programs are meant to align a set of sequences previously gathered using other programs such as blast, fast, sw ...
The main characteristic of T-Coffee is that it will allow you to combine results obtained with several alignment methods. For instance if you have an alignment coming fromClustalW2, an other alignment coming from Dialign, and a structural alignment of some of your sequences, T-Coffee will combine all that information and produce a new multiple sequence having the best agreement whith all these methods.
By default, T-Coffee will compare all you 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 a multiple alignment.