Maligned for the DEC Alpha/VMS

Steve Clark SCLARK at amgen.com
Thu May 9 11:54:43 EST 1996

I have ported the multiple sequence alignment editor, Maligned, to the
DEC Alpha running OpenVMS. In the past I have had a couple of queries about
the availability of an Alpha version. If there is enough interest, I'll 
look into posting it to an FTP site somewhere. If you're currently running
the VAX version and are thinking about moving to the Alpha and want to 
take Maligned along, please drop me a line.

For those of you who aren't familiar with Maligned, it is a multiple sequence
alignment editor that highlights matching areas on the screen in one of
several ways. As you edit the alignment (insert gaps and slide one sequence
against the others) the highlighting changes to reflect the new matches.
Principly it is used by importing an MSF file (created by the GCG program
Pileup, for example), editing and formatting it to highlight the (mis)matching
areas. Hardcopy output can be generated for PostScript, HP and some
other printers that show the highlighted matching regions.

For a more thorough description including pictures, check out the
reference "MALIGNED: a multiple sequence alignment editor" (1992) CABIOS
vol 8 # 6, pa 535.

Stephen Clark, Ph.D.                                sclark at amgen.com

Research Scientist
Department of Computational Biology                 (805) 447-1982 (fax)
Amgen Corp, Mailstop 14-1-D
Amgen Center
Thousand Oaks, California
U.S.A.  91320

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