Alignment Window Edit Menu

• Undo
  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
  Any actions which you undo can be redone using redo.
• Cut
  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
  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 is a tab separated list
  NAME START_RES END_RES SEQUENCE
• Paste
  • To New Alignment
    A new alignment window will be created from sequences previously copied or cut to the system clipboard.
    Use <CTRL> and V(<APPLE> and V on MacOSX) to paste.
  • Add To This Alignment
    Copied sequences from another alignment window can be added to the current Jalview alignment.
• Delete
  This will delete the currently selected residues without copying them to the clipboard. Like the other edit operations, this can be undone with Undo.
• Select All
  Selects all the sequences and residues in the alignment.
  Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.
• Deselect All
  Removes the current selection box (red dashed box) from the alignment window. All selected sequences, residues and marked columns will be deselected.
  Use <ESCAPE> to deselect all.
• Invert Selection
  Any sequence ids currently not selected will replace the current selection.
• Undefine Groups
  The alignment will be reset with no defined groups.
  WARNING: This cannot be undone.
• Remove Left
  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
  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 Empty Columns
  All columns which only contain gap characters ("-", ".") will be deleted.
  You may set the default gap character in preferences.
• Remove All Gaps
  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
  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 no empty columns before or after the first or last aligned residue) and all sequences will be padded with gap characters to the 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.