Contents

• Introduction
  • About this document
    • Credits
    • Reproduction
  • What is EMBOSS?
    • Where to get it?
  
  
• Installation
  • Retrieving EMBOSS by anonymous ftp
    • Interactive FTP
    • FTP using wget
  • Unpacking
  • Graphics Requirements
    • zlib
    • libpng
    • gd
  • Compilation
    • Configure
    • Configuring for 64 bit systems
    • Building EMBOSS
    • Post compilation setup
    • EMBOSS data files
    • Testing your EMBOSS installation
  • Installing EMBASSY
    • EMBASSY package specific notes
  • Installing EMBOSS in package format
    • Installing EMBOSS on FreeBSD
  
  
• Configuration
  • EMBOSS environment variables
    • Configuring EMBOSS differently for different groups of users
  • Databases
    • Database access modes
    • General database configuration.
    • Mixed access methods
    • Indexing and configuring flatfile databases
    • Fine tuning the installation:
    • Indexing and configuring GCG format databases
    • Indexing and configuring BLAST databases
    • Indexing and configuring FASTA databases
    • Configuring EMBOSS to use SRS for database lookup.
    • Indexing and configuring other databases
  • Other data
    • REBASE
    • TRANSFAC
    • PROSITE
    • PRINTS
    • AAINDEX
    • CUTG
    • Miscellaneous data files
  • Default program settings
  • Logging
  
  
• Graphical interfaces to EMBOSS
• Resources
  • Web sites
    • Programs
    • Databases
    • Other Documentation
  • Maintainance of your EMBOSS installation
    • Automated installation of EMBOSS and EMBASSY
    • Automated database updating
  
  
• GNU Free Documentation License
• Acknowledgements