+<p><strong>THE ANNOTATION FILE FORMAT</strong>
+<br/>An annotation file consists of lines containing an instruction followed by
+tab delimited fields. Any lines starting with "#" are considered comments, and
+ignored. The sections below describe the structure of an annotation file.
+</p><ul>
+<li><a href="#annheader">JALVIEW_ANNOTATION</a> mandatory header</li>
+<li><a href="#annrows">LINE_GRAPH, BAR_GRAPH and NO_GRAPH</a> to create annotation rows</li>
+<li><a href="#combine">COMBINE, COLOUR and GRAPHLINE</a> for thresholds and complex line graphs</li>
+<li><a href="#annrowprops">ROWPROPERTIES</a> control the display of individual annotation rows</li>
+<li><a href="#groupdefs">SEQUENCE_GROUP</a> to define groups of sequences for further annotation</li>
+<li><a href="#groupprops">PROPERTIES</a> to set visualisation properties for sequence groups</li>
+<li><a href="#seqgrprefs">SEQUENCE_REF and GROUP_REF</a> for specifying target sequences and groups for annotation, reference sequence and column visibilty commands.</li>
+ <li><a href="#refsandviews">VIEW_SETREF, VIEW_HIDECOLS and HIDE_INSERTIONS</a>
+ for assigning the reference sequence on the alignment and hiding columns.</li>
+ </ul>
+ <p>
+ At the end of this document, you can also find notes on <a
+ href="#compatibility">compatibility</a> of annotation files across
+ different versions of Jalview. An <a href="#exampleann">example
+ annotation file</a> is also provided along with instructions on how to
+ import it to Jalview.
+ </p>
+ <hr/>
+<p><strong><em><a name="annheader">Header line</a></em></strong><br/>The first non-commented out line of a valid Annotations file
+must begin with :<strong><pre>JALVIEW_ANNOTATION</pre></strong></p>
+<hr/>
+<p><strong><em><a name="annrows">LINE_GRAPH, BAR_GRAPH and NO_GRAPH</a></em></strong><br/>
+Labels, secondary structure, histograms and line graphs are added with a line like <strong><pre><em>GRAPH_TYPE</em>	<em>Label</em>	<em>Description</em> (optional)	<em>Values</em></pre></strong></p>
+ <p>
+ Here, the <em>GRAPH_TYPE</em> field in the first column defines the
+ appearance of the annotation row when rendered by Jalview. The next
+ field is the row <em>label</em> for the annotation. This may be
+ followed by a <em>description</em> for the row, which is shown in a
+ tooltip when the user mouses over the annotation row's label. Since
+ Jalview 2.7, the description field may also contain HTML tags (in the same
+ way as a <a href="featuresFile.html">sequence feature's</a> label),
+ providing the text is enclosed in an <html/> tag.
+
+ <ul><em>Please note: URL links embedded in HTML descriptions are not yet supported.</em>
+ </ul>
+ </p>
+ <p>
+ The final <em>Values</em> field contains a series of "|"
+ separated value fields. Each value field is itself a comma separated
+ list of fields of a particular type defined by the annotation row's <em>GRAPH_TYPE</em>.
+ The allowed values of <em>GRAPH_TYPE</em> and corresponding
+ interpretation of each <em>Value</em> are shown below:
+
+ <ul>
+ <li><strong>BAR_GRAPH</strong><br> Plots a histogram with
+ labels below each bar.<br> <em>number</em>,<em>text
+ character</em>,<em>Tooltip text</em></li>
+ <li><strong>LINE_GRAPH</strong><br> Draws a line between
+ values on the annotation row.<br> <em>number</em></li>
+ <li><strong>NO_GRAPH</strong><br>For a row consisting of
+ text labels and/or secondary structure symbols.<br> <em>{Secondary
+ Structure Symbol}</em>,<em>text label</em>,<em>Tooltip text</em><br /> <br />The
+ type of secondary structure symbol depends on the alignment being
+ annotated being either Protein or RNA. <br />For proteins, structure
+ symbols are <em>H</em> (for helix) and <em>E</em> (for strand)<br />
+ <br />For RNA structures, VIENNA, WUSS, and extended notations can
+ be used to specify paired positions.
+ <ul>e.g. "(|(||)|)" or "|A|A|A|(|a|a|a|)")
+ </ul></li>
+ </ul>
+ Any or all value fields may be left empty, as well as the BAR_GRAPH's
+ text character field, and either or both of the text-label and
+ secondary structure symbol fields of the NO_GRAPH type annotation rows.
+ </p>
+<p>Color strings can be embedded in a value field by enclosing an RGB triplet in square brackets to colour that position in an annotation row.