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-
-
-
-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.
-
-
-
-