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!
Geoff.
--------------------------------------------------------------------------------
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
U.K.
--------------------------------------------------------------------------------
