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.

NOTE
The default row length is 100 residues. If you want to change that to
something else (e.g. 1000) pass ROW=1000 to the script.

OPTIONAL
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.

CITING
Bond, C.S. and Schuttelkopf, A.W. (2009), Acta cryst. D65, 510-512