3.2. Navigating the Application Documentation

3.2.1. Navigating the Tabular Documentation

The application documentation is available online in an editable form from the EMBOSS Wiki:


You will see a link for "Application documentation templates". Follow that link now.

You'll see a page where all of the applications are listed in alphabetical order. Scroll down the page and follow the link to seqret. This will bring up the full documentation for the seqret application. The documentation there is organised into sections (see below). You can contribute to EMBOSS by adding to and improving the documentation.

3.2.2. Sections in the Application Documentation

The sections in the application documentation are as follows:


Application name is given after 'Appdoc:'.


Terse, formal description of application inputs, outputs and functionality.


Description of the application suitable for the general user.


Usage example(s) which are command line sessions generated automatically from test cases used for application quality assurance.

Command line arguments

Synopsis of how to use the application at the command line presented as a table of command-line qualifiers.

Input file format

Example input files generated automatically from the test cases. A description of the input files (e.g. file formats) or URL linking to them is sometimes given.

Output file format

Example output files generated automatically from the test cases. A description of the output files or URL linking to them is sometimes given.

Data files

Data files generated automatically from the ACD files. A description of the data files or URL linking to them is sometimes given.


Peripheral documentation such as usage notes.


Technical description of the algorithm. This section is not always present.


Literature references and instructions on how to cite the application.


Cautionary usage advice.

Diagnostic error messages

Diagnostic warning and error messages the application might generate.

Exit status

Values the application might generate (and pass to the operating system) upon exiting.

Known bugs

Known bugs or issues with the application.

See Also

List of links to applications in the same group.


Author details, often just "EMBOSS" is given reflecting the collaborative nature of the project.


Application revision history, including date of last revision, name of revising author and brief remarks about the revision.

Target users

The type of end-user (for example biologist, bioinformatician or system administrator) the application is intended for.


Miscellaneous comments not covered by the categories above.