Alignment Annotation

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 option.

Types of annotation

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
Individual and 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 menu.

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).

Editing labels and secondary structure annotation rows

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 menu:

User defined annotation is stored and retrieved using Jalview Archives.

Current Limitations

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 file.