New version of Maligned available

Thu May 28 02:40:13 EST 1992

	Version 1.65b of Maligned is now available. This fixes a couple of 
bugs from version 1.64 and makes a couple of changes to speed up the screen 
display. For more details, the release notes are appended to the end of
this message. For those of you who don't know what Maligned is, a short
description, taken from the readme file, precedes the release notes. 

	The program is available from the EMBL mail server 
(netserv at and by FTP from and Check out the .../incoming directory for 
maligned_v1_65b.uue. NOTE: Make sure you get version 1.65b and not version 

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

	In anticipation of the inevitable question, Maligned is still 
available only for VAX/VMS systems.

Steve Clark

clark at  (Internet)
clark at salk               (Bitnet)

------------------------- from the readme file --------------------------

	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. 

------------------------- from the release notes ------------------------

To update to the newest version of Maligned when you have properly
installed and configured a previous version, just replace the file
MALIGNED.EXE and possibly the appropriate help file if new features have
been added to the program. First-time users should refer to the
instructions in the file INSTALL_MALIGNED.TXT. 

Revisions to Maligned:

Version 1.65b	May 16, 1992

Bugs fixed:

- Exporting an alignment to a Lineup file which had been imported from an
MSF file no longer crashes the program. (This bug was introduced in 
version 1.65.)

Version 1.65    May 8, 1992

Added features

- The commands "set term/update" and "set term/noupdate" were added. The 
"/update" qualifier, which is the default (and is not saved with the
alignment), sets the program to update the highlighting of the relevant
region of the WHOLE alignment whenever an edit is made. The "/noupdate" 
qualifier sets the program so just the sequence which is being edited is 
updated and the rest of the alignment, including the consensus line if 
displayed, is left as is. This cuts down on the amount of screen redrawing 
and significantly speeds things up when working on large alignments. With 
large alignments, editing one sequence has little effect on the quality of 
the rest of the alignment. The command <Ctrl>r can be used to redraw the
entire screen whenever necessary. 


- To further speed up the editing process, unnecessary screen redraws after 
entering a single command-line command have been eliminated.

Bugs fixed:

- When exporting an msf file from an alignment that had been imported from 
an msf file, the program would crash. This was fixed by adding a period (.) 
to the filenames of the imported msf sequences.
- Only about the first 1000 bases of long sequences could be added to the 
alignments. Now up to 10000 bases, as reported in the manual, can be added. 
- When the consensus line was displayed, changing to Lineup mode would turn 
off the consensus calculation but the old consensus line would remain on 
the screen. Now switching to Lineup mode does not disable the consensus 

Version 1.64	October 4, 1991

Added features:

- GCG Multiple Sequence Format files (MSF) can be exported with the command
"export msf"
- The "import/pileup" command was changed to "import/msf"

Bugs fixed:

- Maligned would sometimes crash when the "print" command was issued and
the printer styles hadn't been properly defined for the output device. This 
usually occured when an alignment was generated when one output device was
specified in the configuration file, and was printed when the configuration
file specified a different output device. Maligned now checks the validity
of printer highlighting styles before printing.

Version 1.63	August 17, 1991

Added features:

- the qualifier "/HISTOGRAM" was added to the "set consensus" command. This
only has an effect when in quantify mode

Bugs fixed:

- when switching to differences mode with the consensus sequence displayed,
the consensus was still displayed, although not updated.
- highlighting wasn't properly updated when scrolling vertically and the 
cursor was not on the first column of the screen

Version 1.62b	August 12, 1991

Bugs fixed:

- "export/phylip" command would give output conversion error if the distance
value was >9.999. This was fixed by setting the maximum value to 9.999
- "export/phylip/nogaps" gave nonsense in the output file

Version 1.62	July 12, 1991

Features added:

- the "/SUMMARY" qualifier was added to the "stats" command

Version 1.61b	July 10, 1991

Bugs fixed:

- "print" command gave output conversion error on sequences with three digits 
in their number (ie, sequences >99)
- "stats" command redirected the screen output to a file if there were more
than 110 sequences in the alignment

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