Popup Menu
This menu is visible when right clicking either within a selected region on the alignment, on a sequence name, and also when right-clicking a sequence feature. It may not be accessible when in 'Cursor Mode' (toggled with the F2 key).
Mac Users: pressing CTRL whilst clicking the mouse/track pad is the same as a right-click. See your system's settings to configure your track-pad's corners to generate right-clicks.

- Selection
  This menu is only visible when right-clicking a selected sequence or region of the alignment.
  - Sequence Details...
    (Since Jalview 2.8)
    Open an HTML report containing the annotation and database cross references normally shown in the sequence's tooltip.
  - Show Annotations...
    Choose to show (unhide) either All or a selected type of annotation for the selected sequences. (Since Jalview 2.8.2)
  - Hide Annotations...
    Choose to hide either All or a selected type of annotation for the selected sequences. (Since Jalview 2.8.2)
  - Add Reference Annotations
    Add to the alignment window any annotations on the selected sequences which have been read from reference sources or calculated (for example, secondary structure derived from 3D structure). (Since Jalview 2.8.2)
  - Edit
    - Copy
      Copies the selected region. In the applet version, the copied sequences are not available to the system clipboard.
    - Cut
      Cuts the selected region from the alignment. In the applet version, the copied sequences are not available to the system clipboard.
    - Edit Sequence
      Edit the selected sequence(s) directly. Spaces will be converted to the current gap character.
    - To Upper Case
      Changes the case of selected region to lower case.
    - To Lower Case
      Changes the case of selected region to upper case.
    - Toggle Case
      Switches the case of all residues within the selected region.
  - Output to Textbox
    The selection area will be output to a a text window in the selected alignment format.
  - Create Sequence Feature...
    Opens the dialog box for creating sequence features over the currently selected region on each selected sequence.
  - Create Group
    This will define a new group from the current selection.
  - Remove Group
    This will undefine the selected group.
  - Edit (New) Group
    Group Editing Menu
    Options in this menu modify the name and display properties of the currently selected group, or a new group defined using the current selection.
    - Name: <Group> or Edit name and description
      The first entry in the menu displays the name for the currently selected group, if it has one. Selecting this option opens a window allowing the name and description for this group to be edited. Click OK to set the new name and decription, and cancel to leave the existing name and description unchanged.
    - Group Colour
      Sets the colour of the group.
    - Boxes
      If selected the background of a residue within the selected group will be coloured according to the assigned colour scheme.
    - Text
      If selected the selected group will display text.
    - Colour Text
      If selected the selected group will display text in a colour slightly darker than the background colour of that residue.
    - Border Colour
      Selecting this will display a "Colour Chooser" window. Select a colour than press OK to set the border colour of a group.
    - Show Unconserved
      When this is selected, all symbols in the group matching the consensus sequence at that column will be rendered as a '.', highlighting mutations in the group area.
- Sequence Id
  This menu is only visible if you right-click on a sequence name.
  - Sequence Details ...
    (Since Jalview 2.8)
    Open an HTML report containing the annotation and database cross references normally shown in the sequence's tooltip.
  - Edit Name/Description
    You may edit the name and description of each sequence. A window will be displayed asking for a new sequence name and sequence description to be entered. Press OK to accept your edit. To save sequence descriptions, you must save in Fasta, PIR or Jalview File format.
  - Add Reference Annotations
    When enabled, copies any available alignment annotation for this sequence to the current view.
  - Set as Reference or Unmark as Reference
    Sets or unsets the reference sequence for the the alignment.
  - Represent Group With (Sequence Id)
    All sequences in the current selection group will be hidden, apart from (Sequence Id). Any edits performed on the visible representative sequence will be propagated to the hidden sequences.
  - Link
    This menu item lists all links which have been set up in the Preferences Connections tab.
    Since Jalview 2.4, links will also be made for database cross references (where the database name exactly matches the link name set up in Preferences).
    Since Jalview 2.5, links are also shown for non-positional sequence features attached to the sequence, and any regular-expression based URL links that matched the description line.
- 3D Structure Data... This menu is visible when you right-click on a sequence name. When this option is clicked, Jalview will open the 'Structure Chooser' , which allows you to discover and view 3D structures for the current selection. For more info, see viewing PDB structures.
- VARNA 2D Structure
  If the sequence or alignment has RNA structure, then VARNA 2D Structure entries will also be present enabling you to open a linked view of the RNA structure in VARNA.
- Hide Insertions
  Hides columns containing gaps in both the current sequence and selected region, and reveals columns not including gaps. (before 2.10.2, this option hid or revealed columns according to gaps in just the current sequence)
- Hide Sequences
  Hides the currently selected sequences in this alignment view.
- Feature Details
  Each entry opens a Sequence Feature Report for visible features under the mouse.
  Only visible when right-clicking a region where Sequence Features are shown.