This menu is visible
when right clicking either within a selected region on the
alignment or on a selected sequence name. It may not be accessible
when in 'Cursor Mode' (toggled with the F2 key).
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.
(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
- Hide Annotations...
Choose to hide either All or a selected type of
annotation for the selected sequences. (Since Jalview 2.8.2)
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)
selected region. In the applet version, the copied
sequences are not available to the system clipboard.
Cuts the selected region from the alignment. In the
applet version, the copied sequences are not available
to the system clipboard.
- Edit Sequence
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
- To Lower Case
Changes the case of selected region to upper case.
- Toggle Case
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.
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
- Remove Group
This will undefine the selected group.
- Edit (New) Group
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
- Group Colour
Sets the colour
of the group.
If selected the background of a residue within the
selected group will be coloured according to the
assigned colour scheme.
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
- 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
- Sequence Id
This menu is only visible if you right-click on a sequence
- 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
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
currently selected sequences in this alignment view.