-<html>\r
-<body>\r
-<p><strong>Conservation Calculation</strong></p>\r
-<p>This option is based on the AMAS method of multiple sequence alignment analysis \r
- (Livingstone C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy \r
- for the Hierarchical Analysis of Residue Conservation.CABIOS Vol. 9 No. 6 (745-756)). \r
- <br>\r
- Hierarchical analysis is based on each residue having certain physico-chemical \r
- properties. </p>\r
-<p>The alignment can first be divided into groups. This is best done by first \r
- creating an average distance tree (Calculate->Average distance tree). Selecting \r
- a position on the tree will cluster the sequences into groups depending on the \r
- position selected. Each group is coloured a different colour which is used for \r
- both the ids in the tree and alignment windows and the sequences themselves. \r
- If a PCA window is visible a visual comparison can be made between the clustering \r
- based on the tree and the PCA. </p>\r
-<p>The grouping by tree may not be satisfactory and the user may want to edit \r
- the groups to put any outliers together. </p>\r
-<p>The existing colour scheme is modified so that the most conserved columns in \r
- each group have the most intense colours and the least conserved are the palest</p>\r
-<p>The conservation analysis is done on each sequence group. This highlights differences \r
- and similarities in conserved residue properties between groups. </p>\r
-<p></p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+-->
+<head><title>Alignment Conservation Annotation</title></head>
+<body><p><strong>Alignment Conservation Annotation</strong></p>
+<p>This is an automatically calculated quantitative alignment
+annotation which measures the number of conserved physico-chemical
+properties conserved for each column of the alignment. Its calculation
+is based on the one used in
+ the AMAS method of multiple sequence alignment analysis :<br>
+<ul>Livingstone
+ C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy
+ for the Hierarchical Analysis of Residue Conservation.<em>CABIOS</em> Vol. <b>9</b>
+ No. 6 (745-756)).
+</ul>
+</p>
+<p>Conservation is measured as a numerical index reflecting the conservation of
+ <a href="../misc/aaproperties.html">physico-chemical
+ properties</a> in the alignment: Identities score highest, and the next most
+ conserved group contain substitutions to amino acids lying in the same physico-chemical
+ class.</p>
+
+<p><em>Colouring an alignment by conservation</em><br>
+Conservation scores can be used to colour an alignment. This is
+explained further in the help page for <a
+href="../colourSchemes/conservation.html">conservation colouring</a>.
+</p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff