Alignment Window Menus

Alignment Window Edit Menu

- Undo (Control Z)
  This will undo any edits you make to the alignment. This applies to insertion or deletion of gaps, cutting residues or sequences from the alignment or pasting sequences to the current alignment or sorting the alignment. NOTE: It DOES NOT undo colour changes, adjustments to group sizes, or changes to the annotation panel.
- Redo (Control Y)
  Any actions which you undo can be redone using redo.
- Cut (Control X)
  This will make a copy of the currently selected residues before removing them from your alignment. Click on a sequence name if you wish to select a whole sequence.
  Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.
- Copy (Control C)
  Copies the currently selected residues to the system clipboard - you can also do this by pressing <CTRL> and C (<APPLE> and C on MacOSX).
  If you try to paste the clipboard contents to a text editor, you will see the format of the copied residues FASTA.
- Paste
  - To New Alignment (Control Shift V)
    A new alignment window will be created from sequences previously copied or cut to the system clipboard.
    Use <CTRL> and <SHIFT> and V(<APPLE> and <SHIFT;> and and V on MacOSX) to paste.
  - Add To This Alignment (Control V)
    Copied sequences from another alignment window can be added to the current Jalview alignment.
- Delete (Backspace)
  This will delete the currently selected residues without copying them to the clipboard. Like the other edit operations, this can be undone with Undo.
- Remove Left (Control L)
  If the alignment has marked columns, the alignment will be trimmed to the left of the leftmost marked column. To mark a column, mouse click the scale bar above the alignment. Click again to unmark a column, or select "Deselect All" to deselect all columns.
- Remove Right (Control R)
  If the alignment has marked columns, the alignment will be trimmed to the right of the rightmost marked column. To mark a column, mouse click the scale bar above the alignment. Click again to unmark a column, or select "Deselect All" to deselect all columns.
- Remove Empty Columns (Control E)
  All columns which only contain gap characters ("-", ".") will be deleted.
  You may set the default gap character in preferences.
- Remove All Gaps (Control Shift E)
  Gap characters ("-", ".") will be deleted from the selected area of the alignment. If no selection is made, ALL the gaps in the alignment will be removed.
  You may set the default gap character in preferences.
- Remove Redundancy (Control D)
  Selecting this option brings up a window asking you to select a threshold. If the percentage identity between any two sequences (under the current alignment) exceeds this value then one of the sequences (the shorter) is discarded. Press the "Apply" button to remove redundant sequences. The "Undo" button will undo the last redundancy deletion.
- Pad Gaps
  When selected, the alignment will be kept at minimal width (so there are no empty columns before or after the first or last aligned residue) and all sequences will be padded with gap characters before and after their terminating residues.
  This switch is useful when making a tree using unaligned sequences and when working with alignment analysis programs which require 'properly aligned sequences' to be all the same length.
  You may set the default for Pad Gaps in the preferences.