Is T-Coffee different from ClustalW?
According to several benchmarks, T-Coffee appears to be more accurate than ClustalW. Yet, this increased accuracy comes at a price: T-Coffee is slower than Clustal (about N times). If you are familiar with ClustalW, or if you run a ClustalW server, you will find that we made some efforts to ensure as much compatibility as possible between ClustalW and T-COFFEE. Whenever it was relevant, we have kept the flag name and the flag syntax of ClustalW. Yet, you will find that T-Coffee also has many extra possibilities If you want to align closely related sequences, T-Coffee can also be used in a fast mode, much faster than ClustalW, and about as accurate ( T-Coffee -very_fast) This mode is especially useful to align long sequences.
