Program(s) for boxing sequence symbols in multiple alignments?

Kay Hofmann KHOFMANN at cipvax.biolan.Uni-Koeln.DE
Thu Mar 19 11:26:44 EST 1992

In <1992Mar18.221140.3114 at athena.cs.uga.edu> WEISE at gandal.dnet@server.uga.edu writes:

> 	Is there software that will allow one to highlight (by boxing or
> otherwise) AAs in sequences that are in multiple alignments so that those
> agreeing with a concensus can easily be identified?  It would also be nice if
> such a program could offer the ability to differently highlight residues that
> represent conservative substitutions.  Alignments annotated in this manner are
> quite often published.
> hand.

To my knowledge, there are three public domain programs available at the
moment that may suit your task:

- The program PRETTYBOX, written by Rick Westermann at Purdue is embedded in
  the GCG sequence analysis package and offers many possible output options
  if you have your multiple aligned sequences in GCG compatible format and
  are using VAX/VMS computers and a POSTSCRIPT output device. 
  It is available by ftp from ftp.bio.indiana.edu and 
  nic.funet.fi and probably from many other places. 

- The program BOXSHADE, written by myself, exists for VAX/VMS and MSDOS
  computers. Besides GCG, it supports  also CLUSTAL, MALIGNED, ESEE and PHYLIP
  format. It also supports different output devices, among them POSTSCRIPT,
  ReGIS, VT, HPGL and some more.
  Its user interface is a little bit clumsy but it will do its work.
  BOXSHADE is availabel from netserv at embl-heidelberg.de and via ftp from
  ftp.bio.indiana.edu and nic.funet.fi

The shading strategies of the two programs are a bit different from each other,
see the documentation for details.

- The multiple alignment editor MALIGNED (i forgot the authors name) has also
  routines for shading its output on POSTSCRIPT printers, i don't know much
  about this program part but MALIGNEDs editor features are very nice.
  As far as i know, MALIGNED is availble from the same source as the other
  programs above

I hope this brief description was fair and helpful,
best regards,

Kay Oliver Hofmann                        Tel. ++49 201 478 6980
Institut fuer Biochemie (med. Fak.)       FAX  ++49 201 478 6979
Universitaet Koeln
Joseph Stelzmann Str. 52            INTERNET:
D-5000 Koeln 41                     KHOFMANN at gen1.genetik.uni-koeln.de

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