-<html>\r
-<head><title>Conservation Calculation</title></head>\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 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<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>
+ <em><a
+ href="http://www.compbio.dundee.ac.uk/papers/amas/amas3d.html"
+ >View an HTML version of the paper</a></em>
+ </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>Conservation is visualised on the alignment or a sequence group
+ as a histogram giving the score for each column. Conserved columns
+ are indicated by '*' (score of 11 with default amino acid property
+ grouping), and columns with mutations where all properties are
+ conserved are marked with a '+' (score of 10, indicating all
+ properties are conserved).</p>
+ <p>
+ Mousing over a conservation histogram reveals a tooltip which
+ contains a series of symbols corresponding to the physicochemical
+ properties that are conserved amongst the amino acids observed at
+ each position. In these tooltips, the presence of <em>!</em> implies
+ that the lack of a particular physicochemical property is conserved
+ (e.g. !proline).
+ </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