Sequence Feature Settings Dialog Box

Select View→Feature Settings... menu entry in an alignment window to open the feature settings dialog box, which allows you to precisely control the presence and appearance of sequence features for the current alignment.

Sequence Feature Settings for the Jalview Application

The top section of the dialog box lists all the sequence feature groups, along with a tickbox for each that controls whether its features are displayed. The table in the middle lists all the features in the currently selected groups, along with their display style and whether they are currently being displayed (only the ticked features and groups are displayed). You can change the colour or shading style used for a feature in the associated alignment by clicking on its colour box.

Feature settings pop-up menu
Right-click on a feature to open a pop-up menu that allows you to sort the alignment or current selection using that feature type (see below), or toggle the type of colouring used for the feature. Features may be highlighted with either a single colour or a feature colourscheme based on either the scores associated with that feature or from the feature's description (e.g. to distinguish different names associated with a DOMAIN feature).

Ordering alignment by features
The 'Seq Sort by Score' and 'Seq Sort by Density' buttons will sort the alignment based on the average score or total number of currently active features and groups on each sequence. To order the alignment using a specific feature type, use the sort by .. entries in the pop-up menu for that type.
Feature sorting and graduated feature colouring was introduced in jalview 2.5

Transparency and Feature Ordering

It is important to realise that sequence features are often not distinct and often overlap (for example, a metal binding site feature may be attached to one position along a stretch of sequence marked with a secondary structure feature).

The ordering of the sequence features in the dialog box list is the order used by jalview for rendering sequence features. A feature at the bottom of the list is rendered below a feature higher up in the list.
You can change the order of a feature by dragging it up and down the list with the mouse.

The Optimise order button (currently only available in the application) will re-order the feature render ordering based on the average length of each feature type.

The transparency slider setting (currently only available in the application version) controls the visibility of features rendered below other features. Reducing the transparency will mean that features at the top of the list can obscure features lower down, and increasing it allows the user to 'see through' the upper layers of a set of features.

You can save all features, with their current colours and visibility in a Jalview format file.