Software packages, where they are mentioned, appear in this format. For example:
HMMER is an EMBASSY package that wraps third party applications.
Applications, where they are mentioned, appear in this format. For example:
seqret is an example of an EMBOSS program.
Options to programs appear like this:
-help
Interfaces, where they are mentioned, appear in this format. For example:
Jemboss is an example of an EMBOSS interface.
The name of a database, or parts of a database, appear in this format. For example:
EMBL is an example of a sequence database.
Specific EMBOSS system files or directories appear in this format. For example:
.embossrc and emboss.default are EMBOSS system files.
Environment variables, where mentioned, appear in this format. For example:
EMBOSS_ACDROOT is an EMBOSS environment variable.
All other specific system items appear in this format. For example:
A directory is an example of a system item, for example: /home/auser/emboss/emboss/ajax/