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...)
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
3D-Coffee/Expresso), profile information (PSI-Coffee) or RNA
secondary structures (R-Coffee).

examples are installed in /usr/share/t_coffee/

For detailed information and citation:
T-Coffee: A novel method for multiple sequence alignments.
Notredame, Higgins,Heringa,JMB,302(205-217)2000