ClustalW is a maultipe sequence alignment program for DNA or proteins. The online version at EMBL-EBI accepts a variety of input format. For details read the help page for ClustalW.

A HMM-based multiple alignment tool can be found at http://www.soe.ucsc.edu/research/compbio/HMM-apps/tubeup-alignment.html.

For pretty printing of the multiple alignments, see Shading of multiple sequence alignments.