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<p><strong>Sequence Feature Settings Dialog Box</strong></p>
-<p>Select <strong>View→Feature Settings...</strong> 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.</p>
-<center>
- <img src="featureSettings.gif" width="351" height="350"> <br>
- Sequence Feature
- Settings for the Jalview Application</img></center>
+<p>Select <strong>View→Feature Settings...</strong> 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.</p>
+<center><img src="featureSettings.gif" width="351" height="350">
+<br>
+Sequence Feature Settings for the Jalview Application</img></center>
<p>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 they are currently being displayed (only the
- ticked features and groups are displayed). <strong><em>You can change the
- colour used for a feature in the associated alignment by clicking on
- its colour box.</em></strong></p>
-<p><strong>Transparency and Feature Ordering</strong></p><p>
- 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).</p>
-<p>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 <em>below</em> a feature higher
- up in the list.<br><em><strong>You can change the order of a feature
- by dragging it up and down the list with the
- mouse</strong></em>.</p>
-<p>The <strong><em>Optimise order</em></strong> button (currently only available in the application) will re-order the feature render ordering based on the average length of each feature type.</p>
-<p>
- The <strong><em>transparency slider setting</em></strong> (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.</p>
-<p><strong><em>You can save all features, with their current colours and visibility
- in a Jalview format file. </em></strong>
-</p>
+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
+they are currently being displayed (only the ticked features and groups
+are displayed). <strong><em>You can change the colour used
+for a feature in the associated alignment by clicking on its colour box.</em></strong></p>
+<p><strong>Ordering alignment by features</strong><br>
+Right click on a feature type to order the alignment by either the
+feature's score, or the number of features of that type. The 'Order by
+Score' and 'Order by Density' buttons will order the alignnment based on
+the average score or total number of currently active features and
+groups on each sequence. (Experimental - added in jalview 2.4.1)</p>
+<p><strong>Transparency and Feature Ordering</strong></p>
+<p>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).</p>
+<p>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 <em>below</em> a feature higher up in
+the list.<br>
+<em><strong>You can change the order of a feature by
+dragging it up and down the list with the mouse</strong></em>.</p>
+<p>The <strong><em>Optimise order</em></strong> button (currently
+only available in the application) will re-order the feature render
+ordering based on the average length of each feature type.</p>
+<p>The <strong><em>transparency slider setting</em></strong>
+(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.</p>
+<p><strong><em>You can save all features, with their
+current colours and visibility in a Jalview format file. </em></strong></p>
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