-<html>\r
-<head><title>Conservation Calculation</title></head>\r
-<body>\r
-<p><em>Conservation Colours</em></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>When the conservation option is selected the existing colour scheme is modified\r
- so that the most conserved columns in each group have the most intense colours\r
- and the least conserved are the palest.</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>Colouring by Conservation</title>
+</head>
+<body>
+ <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