I think "DNA Star" does better than pretty. It is PC based and very simple
On 31 Oct 1996, Les Klimczak wrote:
>> We are trying to become less dependent on the GCG package,
> especially since many PC- and Web-based programs provide parts of its
> functionality and the fees/costs of maintaining GCG have not declined in
> a noticable way. Our only "missing link" in making graphically enhanced
> sequence alignments in the function of PRETTY - identification of similar
> amino acids, as defined by a similarity matrix such as PAM250, and
> labeling of the identified ones with uppercase.
> Does anyone know of any stand-alone program/macro/script that
> would perform this function? TIA.
>> Les Klimczak
> Dr. Les J. Klimczak | mailto:lklimcza at sas.upenn.edu> Department of Biology | http://www.sas.upenn.edu/~lklimcza> University of Pennsylvania | Tel.: (215) 898 3673
> Philadelphia, PA 19104-6018 | FAX: (215) 898 8780