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  • "New" is a submenu which allows the user to create new trees, models, genetic codes and charts. For details on these objects refer to the upcoming HYPHY GUI documentation.
  • "Open" is a submenu which allows the user to open batch language, tree, data, comma separated (as charts) and text files, and recently opened batch laguage files.
  • "Save" When invoked for the 1st time, prompts the user to select a destination and then saves the contents of the console window to that destination. Consecutive calls write the contents of the console window directly to the previously selected file.
  • "Page Setup" brings up the standard page setup dialog for the currently active printer.
  • "Print" brings up the standard print dialog for the currently active printer and prints the contents of the console window to that printer.
  • "Quit" Immediately quits the application. On MacOS X this item has been moved to the 'HYPHY' menu.

        The "File" menu is disabled while any analysis is run. If you wish to quit before the analysis is finished, cancel the execution using the "Cancel Execution" option in the "Analysis" menu and then "Quit" will be undimmed.

 
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002