- Annotation</strong> is not ticked). </p>
-<p>Web services can also add annotation to an alignment (see the
- <a href="../webServices/jnet.html">JNet web service</a>), and as of Jalview 2.08 quantitative and symbolic
- annotations can be added to an alignment via an <a href="annotationsFormat.html">Annotations
- File</a> dragged into the alignment window or loaded from the
- alignment's file menu.</p>
+ Annotation</strong> is not ticked). Any displayed annotation row can be hidden (using the pop-up
+ menu obtained by right-clicking the label), or re-ordered by dragging the label to a new
+ position with the left mouse button.</p>
+<p>
+Web services can also add annotation to an alignment (see the <a
+href="../webServices/jnet.html">JNet</a> and <a
+href="../webServices/proteinDisorder.html">Disorder</a> protein
+structure prediction services), and as of Jalview 2.08 quantitative
+and symbolic annotations can be added to an alignment via an <a
+href="annotationsFormat.html">Annotations File</a> dragged into the
+alignment window or loaded from the alignment's file menu.
+</p>
+<p><a name="seqannots"/><strong>Sequence Reference Annotation</strong>
+</p>
+<p>
+ Sequence reference annotation is created from 3D structure
+ data, and from the results of sequence based prediction of
+ <a href="../webServices/jnet.html">secondary structure</a> and <a
+ href="../webServices/proteinDisorder.html">disordered region</a>
+ prediction methods.
+</p>
+<p><strong>Sequence Group Annotation</strong>
+</p>
+<p>
+ If sequence groups are defined, <a href="../calculations/conservation.html">Conservation</a>
+ and <a href="../calculations/consensus.html">Consensus</a> annotation can be enabled
+ for each group from the <a href="../menus/alwannotation.html">Annotations menu</a>, or can
+ be imported from a Jalview <a href="annotationsFormat.html">Annotations file</a>.
+</p>
+<p><strong>Sequence Selection from Annotation</strong>
+</p>
+<p>
+ Sequences associated with sequence (or sequence group) annotations can be selected by
+ double-clicking the annotation label with these key combinations:
+ <ul>
+ <li>double-click - Select associated sequences (replaces current selection)</li>
+ <li>shift double-click - add sequences to selection</li>
+ <li>Ctrl (Mac CMD) double-click - toggles inclusion of associated sequences in the current selection</li>
+ </ul>
+ Note this also works in combination with manual sequence selection in the alignment.