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*
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-<head><title>Colouring by Conservation</title></head>
-<body>
-<p><em>Colouring by Conservation</em></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>
+-->
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