stand-alone equivalent of PRETTY

Rick Westerman westerm at purdue.edu
Fri Nov 1 08:55:08 EST 1996

>         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.

Pretty per se doesn't do any alignments; nor do the related programs
PrettyBox and PrettyPlot.  The PileUp program does the actual

There are a couple of multiple sequence alignment programs out there.
Clustal is probably the oldest publically available program.

To replace PrettyBox itself I suggest looking at the BoxShade program by
Kay Hoffmann. I'm not sure if there is a PC-based replacement for
PrettyPlot although I suspect there should be.

-- Rick

Rick Westerman                System Manager of the Ag Campus Lab. for
westerm at purdue.edu            Computational Biology (ACLCB) & Sys. Mgr.
Phone: (317) 494-0505         of the Biochemistry department BCHM bldg.  
  FAX: (317) 494-7897         Purdue Univ. W. Lafayette, IN 47907

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