To run SEQUENCE you normally just need to say

java -jar sequence.jar

However, there are some command line options you can specify. The --headless option is used when you want to generate a .png image from an input file without displaying the SEQUENCE screen. To use it you need to provide the option and follow it with the name of a file containing the text describing the diagram. For example:

java -jar sequence.jar --headless my_sequence_diagram.txt

If you don't supply an the --headless option then the first argument on the command line following sequence.jar is taken as the name of the initial directory to offer in the open dialog. For example:

java -jar sequence.jar some_dir/another_dir

Finally, if you want to be able to use the deprecated, though original, LISP style syntax for authoring sequence diagrams you need to supply the --offer_parser_choice option. For example:

java -jar sequence.jar --offer_parser_choice