User Guide to

ALSCRIPT - Sequence alignment to PostScript
Version 2.03

Geoffrey J. Barton

Laboratory of Molecular Biophysics
University of Oxford
Rex Richards Building
South Parks Road
Oxford OX1 3QU
U.K.

Tel: (44) 1865-275368
Fax: (44) 1865-510454
e-mail: gjb@bioch.ox.ac.uk

REFERENCE:
Barton, G. J. (1993),
ALSCRIPT a tool to format multiple sequence alignments
Protein Engineering, Volume 6, No. 1, pp.37-40.

• Contents
• Update History
• Read This First - VERSION 2.0
• Related Programs
• Availability
• Installing ALSCRIPT
• Brief Description of ALSCRIPT
• New Features in Version 1.4.4
• New Features in Version 1.4.5 - Program alsnum
• New Features in Version 2.0
  • New Step 1 Commands
  • New Step 2 Commands
  • New special TEXT commands
• Running ALSCRIPT
  • Basic Use
  • More complex effects - Text Lines, and Masks
• Using Colour
• The MASK command family
  • Summary of mask commands
• Printing ALSCRIPT Files
• Conclusion
• Appendices
  • ALSCRIPT Command Summary
    • STEP 1 COMMANDS
    • REQUIRED STEP 1 COMMANDS
    • OPTIONAL STEP 1 COMMANDS
    • STEP 2 COMMANDS
  • AMPS Block file format
  • PostScript Fonts
  • 386 DOS installation
  • TECHNICAL NOTES
  • Unix Installation
  • VAX/VMS Installation
  • Alternative ways of invoking ALSCRIPT
  • Program Crashes and Known Bugs
  • Wish List for next version!!
  • Acknowledgements
  • References
• About this document ...