Improving and ascertaining the quality of a multiple sequence alignment is a very challenging step in protein sequence analysis. This is particularly the case when dealing with sequences in the twilight zone, i.e. sharing < 30% identity. Here we describe INTERALIGN, a dedicated user-friendly alignment editor including a view of secondary structures and a synchronized display of carbon alpha traces of corresponding protein structures. Profile alignment, using CLUSTALW, is implemented to improve the alignment of a sequence of unknown structure with the visually optimized structural alignment as compared with a standard multiple sequence alignment. Tree-based ordering further helps in identifying the structure closest to a given sequence.