3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
4 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 <head><title>Colouring by Conservation</title></head>
21 <p><em>Colouring by Conservation</em></p>
22 <p>This is an approach to alignment colouring which highlights
23 regions of an alignment where physicochemical properties are
24 conserved. It is based on the one used in
25 the AMAS method of multiple sequence alignment analysis (Livingstone
26 C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy
27 for the Hierarchical Analysis of Residue Conservation.CABIOS Vol. 9
28 No. 6 (745-756)). See the <a href="../calculations/conservation.html">conservation calculation</a> help page for
29 a more thorough explanation of the calculation.
31 <p>For an already coloured alignment, the conservation index at each
32 alignment position is used to modify the shading intensity of the
33 colour at that position. This means that the most conserved columns
34 in each group have the most intense colours, and the least conserved
35 are the palest. The slider controls the contrast between these
37 <p>Conservation can be calculated over all sequences in an alignment, or just
38 within specific groups (such as those defined by
39 <a href="../calculations/tree.html">phylogenetic tree partitioning</a>).
40 The option 'apply to all groups' controls whether the contrast
41 slider value will be applied to the indices for the currently
42 selected group, or all groups defined over the alignment.</p>