-<p>The first set of lines contain type definitions:<strong>
-<pre><em>Feature label</em>	<em>Feature Colour</em></pre> </strong>A feature
-type has a text label, and a colour (specified as a red,green,blue 24
-bit triplet either in hexadecimal (eg. 00ff00) or as comma separated
-numbers (ranging from 0 to 255)). The text label may contain simple HTML
-document body tags if enclosed by "<html></html>"
-and will be rendered as formatted tooltips in the Jalview Application
-(the Jalview applet is not capable of rendering HTML tooltips, so all
-formatting tags will be removed.</p>
+<p>
+The first set of lines contain type definitions:
+
+<pre>
+<strong><em>Feature label</em>	<em>Feature Colour</em>
+<!-- 	<em>Feature links</em> --></strong>
+</pre>
+
+A feature type has a text label, and a colour specification. This
+can be either:
+
+<ul>
+<li>A single colour specified as either a red,green,blue 24 bit
+triplet in hexadecimal (eg. 00ff00) or as comma separated numbers
+(ranging from 0 to 255))</li>
+
+<li>A <a href="featureschemes.html">graduated colourscheme</a>
+specified as a "|" separated list of fields:
+
+<pre>
+[label|]<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<thresholdtype>|[<threshold value>]]
+</pre>
+
+The fields are as follows:
+
+<ul>
+<li><em>label</em><br>
+ Indicate that the feature description should be used to create a
+colour for features of this type.<br>
+<em>Note: if no threshold value is needed then the final '|' may be
+ommitted.<br>
+This keyword was added in Jalview 2.6</em></li>
+
+<li><em>mincolor</em> and <em>maxcolor</em><br>
+ Colour triplets specified as hexadecimal or comma separated values
+(may be left blank for a <em>label</em> style colourscheme, but
+remember to specify the remaining fields)</li>
+
+<li><em>absolute</em><br>
+ An optional switch indicating that the <em>minvalue</em> and
+<em>maxvalue</em> parameters should be left as is, rather than
+rescaled according to the range of scores for this feature
+type.</li>
+
+<li><em>minvalue</em> and <em>maxvalue</em><br>
+ Minimum and maximum values defining the range of scores for which
+the colour range will be defined over. If minvalue is greater than
+maxvalue then the linear mapping will have negative gradient.</li>
+
+<li><em>thresholdtype</em><br>
+ Either "none", "below", or "above". <em>below</em> and
+<em>above</em> require an additional <em>threshold value</em> which
+is used to control the display of features with a score either
+below or above the value.</li>
+</ul>
+</li>
+</ul>
+</p>
+