6. Chapter 6. The EMBOSS Command Line

The EMBOSS command line is the best supported way to launch applications. It is consistent across all applications and provides a simple interface to, and complete control over, the applications. This chapter describes its features, including how to specify values for application options, global command line qualifiers and datatype-specific ones. The powerful Uniform Sequence Address (USA) and Uniform Feature Object (UFO) mechanisms for specifying sequences and sequences features are described.