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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
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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>
git://source.jalview.org / jalview.git / blobdiff