Desktop Menus

• File
  • Input Alignment from (See more on file formats)
    • File
      open file(s) on your local file system
    • URL
      open a file from a website. The URL MUST start with http://
    • Textbox
      copy and paste an alignment into a text window
  • Fetch Sequence
    Shows a dialog window in which you can select known ids from Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by the European Bioinformatics Institute.
  • Save Project
    Saves all currently open alignment windows with their current view settings and any associated trees, as a Jalview Archive (which has a .jar extension).
  • Load Project
    Loads Jalview archives only.
  • Quit
    Close Jalview. Warning - any annotations you have made on alignments will be lost unless you Save your work before quitting.
    
• Tools
  • Preferences
    Change the default visual settings for opening new alignment windows.
    
• Help
  • About
    Displays the version and creation date of the application, as well as acknowledgements and a citation reference.
  • Documentation
    Displays help files as a browseable, searchable set of pages with a table of contents.
    
• Window
  Each time a new window is added to the Jalview Desktop a new menu item will be added to the "Window" menu. If you are working with several alignments, trees or other types of windows use the "Window" menu to bring your window of choice to the top of the pile if it has been hidden by other windows.