As you'll see, the program runs in the window in which GDE was started. GDE is generates the keystrokes that you would normally be typing. Launch GDE from the command line. This is the best way to run gde. Although GDE can read files from any directory, it's best to launch GDE from the directory in which you plan to work.
Output is stored in a temporary file, which is opened in a text editor.
Save As and type in a name for the output. It's a good idea to include a .numseq file extension to indicate that this file is output from numseq. In the latter case, the output will probably need to be modified to conform to the desired input file format eg. Working with circular DNA molecules Circular DNA molecules require a bit of thought. Conceptually, one base must be arbitrarily labeled as 1.