+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Colouring by Conservation</title>
+</head>
+<body>
+ <p>
+ <strong>Colouring by Conservation</strong>
+ </p>
+ <p>
+ This is an approach to alignment colouring which highlights regions
+ of an alignment where physicochemical properties are conserved. It
+ is based on the one used in the AMAS method of multiple sequence
+ alignment analysis (Livingstone C.D. and Barton G.J. (1993), Protein
+ Sequence Alignments: A Strategy for the Hierarchical Analysis of
+ Residue Conservation.CABIOS Vol. 9 No. 6 (745-756)). See the <a
+ href="../calculations/conservation.html"
+ >conservation calculation</a> help page for a more thorough
+ explanation of the calculation.
+ </p>
+ <p>For an already coloured alignment, the conservation index at
+ each alignment position is used to modify the shading intensity of
+ the colour at that position. This means that the most conserved
+ columns in each group have the most intense colours, and the least
+ conserved are the palest. The slider controls the contrast between
+ these extremes.</p>
+ <p>
+ Conservation can be calculated over all sequences in an alignment,
+ or just within specific groups (such as those defined by <a
+ href="../calculations/tree.html"
+ >phylogenetic tree partitioning</a>). The option 'apply to all groups'
+ controls whether the contrast slider value will be applied to the
+ indices for the currently selected group, or all groups defined over
+ the alignment.
+ </p>
+</body>
+</html>