Jeffrey J. Huckaby wrote:
> I am search for a Mac and/or Unix SunOS program that formats
> multiple sequence alignments for publication such that the similar amino
> acids are shaded and the identities are boxed...or some format close to
> this one.
> Any leads would be appreciated....
> Feel free to respond to me directly.
BOXSHADE will do what you want. The program allows up to three levels of shading
(similar/identical/all identical), and produces output in a number of formats,
including PS, EPSF, PICT X-Fig and HPGL. Originally written for VMS, it has been
ported to Ultrix/Solaris by Peter Stockwell (peter at sanger.otago.ac.nz), if this is
what you mean by SunOS (sorry, no experience with Unix OSs).The full source is always
available from the original author Kay Hofmann (ftp: ulrec3.unil.ch dir:
I think it's quite a nice program, but then I'm one of the authors ;-).
Best of luck,
Michael D. Baron
michael.baron at bbsrc.ac.uk