T-Coffee is a multiple sequence alignment package. You can use T-Coffee to align sequences or to combine the output of your favorite alignment methods (Clustal, Mafft, Probcons, Muscle, etc.) into one unique alignment (M-coffee).

T-Coffee can align Protein, DNA and RNA sequences. It is also able to combine sequence information with protein structural information (Expresso), profile information (PSI-Coffee) or RNA secondary structures (R-Coffee).

This multiple sequence alignment web server has been introduced in 2011 NAR web server issue. Read on.

The full list of associated papers is available on the following links: algorithms and servers.

The original T-Coffee paper is: T-Coffee: A novel method for multiple sequence alignments  Notredame, Higgins, Heringa, JMB, 302 (205-217) 2000 - pdf - medline

T-Coffee is a freeware opensource package distributed under the GNU public license.