T-Coffee (Tree-based Consistency Objective Function For alignment Evaluation) is a multiple sequence alignment software using a progressive approach. It generates a library of pairwise alignments to guide the multiple sequence alignment. It can also combine multiple sequences alignments obtained previously and in the latest versions can use structural information from PDB files (3D-Coffee). It has advanced features to evaluate the quality of the alignments and some capacity of identifying occurrence of motifs (Mocca). It produces alignment in the aln format (Clustal) by default, but can also produce PIR, MSF and FASTA format. The input files are always in FASTA format.
Note that what T-Coffee terms "Clustal" format is sufficiently different from the output of ClustalW/X that many programs supporting Clustal format cannot read it; fortunately ClustalX can import T-Coffee output so the simplest fix for this issue is usually to import T-Coffee's output into ClustalX and then re-export.