+GRAPHLINE	<em>graph_name</em>	<em>value</em>	<em>label</em>	<em>colour</em><strong><em>
+</em></strong></pre>
+<h3><font face="Arial, Helvetica, sans-serif">(Since Jalview 2.2.1) SEQUENCE_GROUP</font></h3>
+<p>Groups of sequences can be defined using the tab delimited line</p>
+<pre>SEQUENCE_GROUP Group_Name Group_Start Group_End Sequences</pre>
+<p>The sequences can be defined by alignment index and a range of sequences can
+ be defined in a comma delimited field such as</p>
+<p>2-5,8-15,20,22</p>
+<p>Enter * to select all groups. </p>
+<p>If the alignment indices are not known, enter -1 then a tab delimited list
+ of sequence ids. </p>
+<p>If the SEQUENCE_REF has been defined, the group_start and group_end will be
+ relative to the sequence residue numbering, otherwise the group_start and group_end
+ will be the alignment column indices. </p>
+<p>The group can (optionally) be assigned various visualisation properties via
+ another tab delimited line thus:</p>
+<pre>PROPERTIES Group_name tab_delimited_key_value_pairs
+</pre>
+<p>The key_value_pairs allow you to define a description and to colour the group
+ in various ways. All, none or some of the following values could be used for
+ a group:</p>
+<p>description=Text <br>
+ colour=Helix Propensity<br>
+ pidThreshold=0<br>
+ consThreshold=0<br>
+ outlineColour=red <br>
+ displayBoxes=true<br>
+ displayText=false<br>
+ colourText=false<br>
+ textCol1=black<br>
+ textCol2=black<br>
+ textColThreshold=0<br>
+ idColour=ff3322<br>
+ hide=false<br>
+ hidecols=false</p>
+<ul><li>if the <strong>idColour</strong> property
+is given without specifying a colour scheme with the <strong>colour</strong>
+property, then the idColour will also be used to colour the sequence.</li>
+<li>the <strong>colour</strong> property can take either a colour scheme name,
+ or a single colour specification (either a colour name like 'red' or an RGB
+ triplet like 'ff0066'). If a single colour is specified, then the group
+ will be coloured with that colour.</li>
+ <li><em>New Features in 2.4.1</em></li>
+ <li>hide and hidecols instruct jalview to hide the sequences or columns covered by the group.</li>
+ <li>Sequence associated Groups<br>If a group is defined after a valid
+ <em>SEQUENCE_REF</em> sequence reference statement, the sequence representative
+ for the group will be set to the referenced sequence.<br><strong>Note:</strong> if the <em>hide</em>
+ property is set then only the representative sequence for the group will be shown in the alignment.</li>
+</ul>
+<p> </p>