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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
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+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
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--->
-<head><title>Colouring by Conservation</title></head>
+ * 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><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>
+ <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>
git://source.jalview.org / jalview.git / blobdiff