displaying alignments

Geoff Barton gjb at bioch.ox.ac.uk
Wed Dec 22 07:22:02 EST 1993

You might like to try ALSCRIPT (Barton, G. J., 1993, Prot. Eng., 6, 37-40).
This provides a set of commands for boxing/shading/colouring/font changing
etc and produces PostScript output.  ALSCRIPT does not make assumptions about
what is a consensus, but provides you with a set of tools for formatting
the alignment.  

I can ftp the package to you, or let you know how to pick it up from my 
machine.  Alternatively, send a formatted 3.5" MS-DOS disk for the package
+ DOS executables.

You may also be interested in  AMAS (Analysis of Multiply Aligned Sequences)
just published in CABIOS (Livingstone C.D. and Barton G. J., CABIOS, 1993,
9, 745-756).  This is a system for hierarchical alignment analysis based on 
physico-chemical properties.  One output form uses ALSCRIPT to give a "sensibly"
boxed and shaded alignment.  I'll make an announcement in January about 
availability of this and other programs.

Hope this helps,

Merry Christmas!


Internet:    gjb at bioch.ox.ac.uk      (Janet:  gjb at uk.ac.ox.bioch)

Telephone: [44] (0)865 275368    [ ] Delete when dialling from UK.
Fax:       [44] (0)865 510454    ( ) Delete when dialling from outside UK.

           Dr. Geoffrey J. Barton     
           Laboratory of Molecular Biophysics
	   University of Oxford
           Rex Richards Building
           South Parks Road
           Oxford OX1 3QU

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