Aline: An Extensible WYSIWYG Protein Sequence Alignment Editor for
Publication Quality Figures.

Aline is an interactive perl/tk application which can read common
sequence alignment formats which the user can then alter, embellish,
markup etc to produce the kind of sequence figure commonly found in
biochemical articles.

Please cite:
Bond, C.S. and Schüttelkopf, A.W. (2009), Acta cryst. D65, 510-512

NOTE:
Although not needed for running Aline, clustalw and mkDSSP are 
desirable for its complete functionality. A third tool is CHAINSAW,
part of the CCP4 suite (http://www.ccp4.ac.uk/). Visit the web site
for more information and installation instructions if you want it.