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new version of BOXSHADE available (2.3a)

Kay Hofmann KHOFMANN at cipvax.biolan.Uni-Koeln.DE
Thu Aug 1 10:59:06 EST 1991

To all multiple aligners out there:

I finally decided to release a new version of my BOXSHADE program to the
net. After a quite hectic upgrading phase (upgrade rate = 0.03 vnu/week,
vnu = version number unit) i hope that the program now has arrived at a
point of rest by now. I intended to say that i do not plan major 
modifications in the near future unless some extremely useful features come
to my mind or are suggested by anyone.

For the ones who don't know the program: it doesn't do very much, you have to 
 do most things yourself e.g. sequencing the proteins, doing a multiple 
 alignment etc. The only thing BOXSHADE does is trying to make your multiple 
 alignment look better. It takes as input mutiple aligned sequences in 
 various formats (PRETTY, MSF, CLUSTAL, MALIGNED) and prepares the sequences
 for output to various devices (ReGIS, LJ250, PS, EPS, UIS). The preparation
 includes giving different colors to letters/backgrounds for identical, similar
 or unrelated residues in the sequences. There are some more options, but you
 have to take a look at the program for seeing what it actually does.

For the ones who know version 2.0 (the last one i released to the net):
 the major modifications are listed below: 

2.3   -default parameter management
      -command line parameters
      -option for shading according to similarity to a single sequence
       instead of a consensus sequence
      -support of GCG V7 MSF-format

2.2   -support of sequence numbering in output
      -support of MALIGNED data files

2.1   -output code completely rewritten for allowing easier modification
      -support of ENCAPSULATED POSTSCRIPT output
      -more compact POSTSCRIPT output files
      -multipage output for all devices
      -modifications in PRETTY and CLUSTAL reading routines
       for coping with slightly altered formats

I don't know if this program is useful for anyone but me, but in case:
do with it what you like. It is public domain.

I would appreciate any comment on the program, especially bug reports are
very welcome and will be looked at. Please expect no reply of me before
August 19th, i will be on vacation.

Oh, i forgot: the program will be available from 

- the mailserver netserv at embl-heidelberg.de
- the ftp site ftp.bio.indiana.edu 
  (at the moment in the dir: 'Incoming', hopefully soon at another place)

Have a nice time,

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