In addition to the definition of groups and sequence features,
Jalview can display symbols and graphs under the columns of an
alignment. These annotation tracks are displayed in the annotation
area below the alignment. The annotation area's visibility is
controlled with the View→Show Annotation
Types of annotation
Data displayed on sequence
annotation rows are associated with the positions of a sequence.
Often this is 'Reference annotation' such as secondary structure
information derived from 3D structure data, or from the results of
sequence based prediction of secondary
structure and disorder.
If reference annotation is available for a the currently selected
sequences, it can be shown by selecting the Add
Reference Annotation option in the sequence or selection popup
- Group associated annotation.
be associated with groups defined on the alignment. If sequence
groups are defined, Conservation
annotation can be enabled for each group from the Annotations menu, or can be
imported from a Jalview Annotations
- Alignment associated annotation.
rows associated with columns on the alignment are simply
'alignment annotation'. Controls allow you to interactively
create alignment annotation to add labels and symbols to
alignment columns. Jalview's consensus, conservation and quality
calculations also create histogram and sequence logo annotations
on the alignment.
Importing and exporting annotation
Annotations on an alignment view are saved in Jalview project files.
You can also load Annotations
Files in order to add any kind of quantitative and symbolic
annotations to an alignment. To see an example, use the Export
Features/Annotation option from an alignment window's File menu.
Layout and display controls
groups of annotation rows can be shown or hidden using the pop-up
menu obtained by right-clicking the label. You can also reorder them
by dragging the label to a new position with the left mouse button.
The Annotations menu provides settings controlling
the ordering and display of sequence, group and alignment associated
annotation. The Colour by annotation option in the
colour menu allows annotation to be used to shade the
alignment. Annotations can also be used to select or
hide columns via the dialog opened from the Selection
Sequence Highlighting and Selection from Annotation
A single click on the label of an annotation row
associated with sequences and sequence groups will cause the
associated sequences to be highlighted in the alignment view. Double
clicking the label will select the associated sequences, replacing
any existing selection. Like with other kinds of selection, shift
double-click will add associated sequences, and Ctrl
(Mac CMD) double-click will toggle inclusion of associated
sequences in the selection.
Interactive Alignment Annotation
Annotation rows are added using the Annotation
Label menu, which is obtained by clicking anywhere on the
annotation row labels area (below the sequence ID area).
- Add New Row
Adds a new,
named annotation row (a dialog box will pop up for you to enter
the label for the new row).
- Edit Label/Description
opens a dialog where you can change the name (displayed label),
or the description (as shown on the label tooltip) of the
- Hide This Row
annotation row whose label was clicked in order to bring up the
- Hide All <label>
all annotation rows whose label matches the one clicked. (This
option is only shown for annotations that relate to individual
sequences, not for whole alignment annotations. Since Jalview
- Delete This Row
the annotation row whose label was clicked in order to bring up
- Show All Hidden Rows
all hidden annotation rows.
- Export Annotation (Application
Annotations can be saved to file or
output to a text window in either the Jalview annotations format
or as a spreadsheet style set of comma separated values (CSV).
- Show Values in Text Box (applet
Opens a text box with a list of
comma-separated values corresponding to the annotation
(numerical or otherwise) at each position in the row. This is
useful to export alignment quality measurements for further
- Scale Label To Column(introduced
Selecting this toggles whether column
labels will be shrunk to fit within each column, or displayed
using the view's standard font size.
Editing labels and secondary structure annotation
Use the left mouse button to select a position
along the row that are to be annotated - these regions will be
coloured red. Press Control or shift
in combination with the left-click to either select an additional
position, or a range of positions on the alignment.
Once positions have been selected, use the right
mouse button and select one of the following from the annotation
Marks selected positions with a
helix glyph (a red oval), and optional text label (see below). A
dialog box will open for you to enter the text. Consecutive
ovals will be rendered as an unbroken red line.
Marks selected positions with a
sheet glyph (a green arrow oriented from left to right), and
optional text label (see below). A dialog box will open for you
to enter the text. Consecutive arrows will be joined together to
form a single green arrow.
- RNA Helix (only shown when working with
Marks selected positions
as participating in a base pair either upstream or downstream.
When the dialog box opens, enter a '(' to indicate these bases
pair with columns upstream (to right), and ')' to indicate this
region pairs with bases to the left of the highlighted columns.
Other kinds of base-pair annotation are also supported (e.g. 'A'
and 'a', or '<' and '>'), and Jalview will suggest an
appropriate symbol based on the closest unmatched parenthesis to
If any brackets do not match up, then an orange
square will highlight the first position where a bracket was
found not to match.
Set the text label at the selected
positions. A dialog box will open for you to enter the text. If
more than one consecutive position is marked with the same
label, only the first position's label will be rendered.
Changes the colour of the
annotation text label.
- Remove Annotation
Blanks any annotation
at the selected positions on the row. Note: This
cannot be undone
User defined annotation is stored and retrieved using Jalview Archives.
The Jalview user interface does not support interactive creation and
editing of quantitative annotation (histograms and line graphs), or
to create annotation associated with a specific sequence or group.
It is also incapable of annotation grouping or changing the style of
existing annotation (e.g. to change between line or bar charts, or
to make multiple line graphs). These annotation capabilities are
only possible by the import of an Annotation