Select View→Feature Settings... in an alignment window to open the feature settings dialog box, which allows - precise control the visibility and appearance of sequence features for + precise control of the visibility and appearance of sequence features for an alignment view.
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. When many groups are present, their names may - be truncated, but the full name be shown in a tooltip when the mouse + be truncated, but the full name is shown in a tooltip when the mouse hovers over their checkbox.
Feature colour schemes and filters
@@ -123,11 +123,18 @@
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.
+ 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. A dialog box
+ is shown if there are no features to use for sorting sequences. To
+ order the alignment using a specific feature type, use the
+ sort by .. entries in the pop-up menu for that type.
When
+ a selected region exists, only features lying within the columns
+ containing the selected region will be considered, but all sequences
+ (including those not selected) will be reordered.
Feature sorting and graduated feature colouring were
introduced in Jalview 2.5