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
All gap characters ("-", ".") will be deleted from the alignment.
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
Adds gaps to the end of all the sequences so they are all the same length. This is useful for making a tree using unaligned sequences.
You may set the default gap character in preferences.