+\subsection{Colouring features by score or description
+text}
+\label{featureschemes}
+Sometimes, you may need to visualize the differences in information carried by
+sequence features of the same type. This is most often the case when features
+of a particular type are the result of a specific type of database query or calculation. Here, they may also carry information within their textual description, or most commonly for calculations, a score related to the property being investigated. Jalview can shade sequence
+features using a graduated colourscheme in order to highlight these variations.
+In order to apply a graduated scheme to a feature type, select the `Graduated
+colour' entry in the Sequence feature type's popup menu, which is opened by
+right-clicking the feature type's color in the settings dalog box. Two types
+of colouring styles are currently supported: the default is quantitative
+colouring, which shades each feature based on its score, with the highest
+scores receiving the 'Max' colour, and the lowest scoring features coloured
+with the 'Min' colour. Alternately, you can select the `Colour by label'
+option to create feature colours according to the description text associated
+with each feature. This is useful for general feature types - such as
+Uniprot's 'DOMAIN' feature - where the actual type of domain is given in the
+feature's description.
+
+Graduated feature colour schemes can also be used to exclude low or
+high-scoring features from the alignment display. This is done by choosing your
+desired threshold type (either above or below), using the drop-down menu in the
+dialog box. Then, adjust the slider or enter a value in the text box to set the
+threshold for displaying this type of feature.
+
+The feature settings dialog box allows you to toggle between a graduated and
+simple feature colourscheme using the pop-up menu for the feature type. When a
+graduated scheme is applied, it will be indicated by in the colour column for
+that feature type - with coloured blocks or text to indicate the colouring
+style and a greater than ($>$) or less than ($<$) symbol to indicate when a
+threshold has been defined.
+
+\subsection{Using features to re-order the alignment}
+\label{featureordering}
+The presence of sequence features on certain seqences or in a particular
+region of an alignment can quantitatively identify important trends in
+the aligned sequences. In this case, it is more useful to
+re-order the alignment based on the number of features or their associated scores, rather than simply re-colour the aligned sequences. The sequence feature settings
+dialog box provides buttons two buttons, `Seq sort by Density' and `Seq sort by
+Score' that allow you to reorder the alignment according to the number of
+sequence features present on each sequence, and also according to any scores
+associated with a feature. Each of these buttons uses the currently displayed
+features to determine the ordering, but
+if you wish to re-order the alignment using a single type of feature, then you can do this from the feature type's
+popup menu. Simply right-click the type's style in the Feature Settings dialog
+box, and select one of the {\sl Sort by score} and {\sl Sort by density}
+options to re-order the alignment. Finally, if a specific region is selected,
+then only features found in that region of the alignment will be used to
+create the new alignment ordering.
+
+\exercise{Shading and sorting alignments using sequence features}{
+\label{shadingorderingfeatsex}
+\exstep{Re-load the alignment from \ref{dasfeatretrexcercise}.
+}
+\exstep{Open the
+feature settings panel, and, after first clearing the current
+selection, press the {\em Seq Sort by Density} button a few times.}
+\exstep{Use the DAS fetcher to retrieve the Kyte and Doolittle Hydrophobicity
+scores for the protein sequences in the alignment.
+{\sl Hint: the nickname for the das source is `kd$\_$hydrophobicity'.}}
+\exstep{Change the feature settings so only the hydrophobicity features are
+displayed. Mouse over the annotation and also export and examine the GFF and
+Jalview features file to better understand how the hydrophobicity measurements
+are recorded.}
+\exstep{Apply a graduated colourscheme to the hydrophobicity annotation to
+reveal the variation in average hydrophobicity across the alignment.}
+\exstep{Select a range of alignment columns, and use one of the sort by feature buttons to order the alignment according to that region's average
+hydrophobicity.}
+\exstep{Save the alignment as a project, for use in exercise
+\ref{threshgradfeaturesex}.} }
+
+\exercise{Shading alignments with combinations of graduated feature
+colourschemes}{
+\label{threshgradfeaturesex}
+\exstep{Reusing the annotated alignment from exercise
+\ref{shadingorderingfeatsex}, experiment with the colourscheme threshold to
+highlight the most, or least hydrophobic regions. Note how the colour scheme icon for the feature type changes when you change the threshold type.}
+\exstep{Change the colourscheme so
+that features at the threshold are always coloured grey, and the most
+hydrophobic residues are coloured red, regardless of the threshold value
+({\em hint - there is a switch on the dialog to do this for you}).}
+\exstep{Enable the Uniprot {\em chain} annotation in the feature settings
+display and re-order the features so it is visible under the hydrophobicity
+annotation.}
+\exstep{Apply a graduated colourscheme to the {\em chain}
+annotation so that it distinguishes the different canonical names associated
+with the mature polypeptide chains.}
+\exstep{Export the alignment's sequence features using the Jalview sequence
+feature file format, to see how the different types of graduated feature
+colour styles are encoded. }
+}