ClustalW2 is a general purpose multiple sequence alignment program for
DNA or proteins. It produces biologically meaningful multiple sequence
alignments of divergent sequences. It calculates the best match for the
selected sequences, and lines them up so that the identities,
similarities and differences can be seen. Evolutionary relationships
can be seen via viewing Cladograms or Phylograms. 

WWW: http://www.clustal.org/