Summary: 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. Availability: Windows and Linux packages, as well as source files, are available under the CeCILL free software licensing agreement at the following address: http://www-dsv.cea.fr/content/cea/d_dep/d_diep/d_sbtn/download.htm Contact:[email protected]