README.TXT

	MALIGNED stands for Multiple ALIGNment EDitor. Is is a screen
editor designed to demonstrate sequence similiarity between related genes
or proteins. The regions of similarity in each sequence are highlighted;
the screen is updated to reflect the current similiarity as the alignments
are changed by shifting a sequence relative to the others, or by adding
gaps. This constant visual feedback of the overall alignment makes it easy
to see the effect of changing the alignment. 

     MALFORM is a post-processing program that converts the ".MAL" file 
produced by Maligned to a file that can be printed on a postscript printer. 

	Maligned and Malform run on a VAX/VMS system and were compiled and
linked under VMS v5.3-1. These programs and files are copyrighted by
Stephen Clark, 1992 (c), but may be freely distributed so long as all files
are distributed and without any changes, and no fee is charged. Once
obtained, the configuration, help and document files may be edited to make
them conform to the local environment, and may be further distributed for
the benefit of others with the same output devices. 

	A paper describing Maligned is in press in CABIOS ("Maligned: a 
multiple sequence alignment program," by Stephen P. Clark.)

	Comments, suggestions, bug reports, etc, can be sent to me at the 
indicated address (Internet is prefered).



Stephen Clark                           May 17, 1992

clark@salk-sc2.sdsc.edu  (Internet)
clark@salk               (Bitnet)


     The following files are part of the Maligned package:

README.TXT
	this file.

MALIGNED_DOC.TXT
	documentation on how to use the program, ascii format.

MALIGNED_DOC.PS
	documentation on how to use the program, PostScript format. 

MALIGNED_DOC.WP5
	documentation on how to use the program, WordPerfect version 5.0
format. 

INSTALL_MALIGNED.TXT
	documentation on how to set the program up.

MALIGNED.EXE
	the Maligned program, executable on a VAX running VMS, binary mode.

MALIGNED.COM
	a command procedure to launch the program.

WPMALIGNED.COM
	a command procedure to launch the program, creating a "print" file
that can be read into WordPerfect. 

HPLASER2.CNF
	configuration file for hardcopy output to an HP LaserJet II
printer. 

EPSON-9.CNF
	configuration file for hardcopy output to an Epson 9-pin dot-matrix
printer. 

POSTSCRIPT.CNF
	configuration file for hardcopy output to PostScript laser printer.

WP50.CNF
	configuration file for writing files that can be read by
WordPerfect. 

DEC.HLP
	help file for use with DEC VT100 terminals.

IBM-PC.HLP
	help file for use with an MS-DOS computer running DEC terminal
emulation software. 

MOUSE.MALIGNED
	sample alignment of mouse globin-related sequences.

RELEASE_NOTES_v1_65b.TXT
	description of changes in successive versions of the program.


The following files are part of the Malform package:

MALFORM.EXE
	the Malform program, executable on a VAX running VMS (binary).

MALFORM_DOC.TXT
	Instructions on how to use the program, ascii.

MALFORM_DOC.PS
	Instructions on how to use the program, in PostScript format.

MALFORM_DOC.WP5
	Instructions on how to use the program, in WordPerfect version 5.0 
format.

MALFORM.CNF
	the Malform configuration file.

INSTALL_MALFORM.TXT
	instructions on setting up Malform.

GREYSCALE.PS
	A file to test the capabilities of your PostScript printer.