+
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 colour and whether +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 used -for a feature in the associated alignment by clicking on its colour box.
+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 create a feature colourscheme based on either the
+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 'Order by Score' and 'Order by Density' buttons will order the
+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.
-Feature sorting and colour feature by score and description was
-introduced in jalview 2.4.1
+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