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20 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
21 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
23 * This file is part of Jalview.
25 * Jalview is free software: you can redistribute it and/or
26 * modify it under the terms of the GNU General Public License
27 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
29 * Jalview is distributed in the hope that it will be useful, but
30 * WITHOUT ANY WARRANTY; without even the implied warranty
31 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
32 * PURPOSE. See the GNU General Public License for more details.
34 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
36 <head><title>Colouring by Conservation</title></head>
38 <p><em>Colouring by Conservation</em></p>
39 <p>This is an approach to alignment colouring which highlights
40 regions of an alignment where physicochemical properties are
41 conserved. It is based on the one used in
42 the AMAS method of multiple sequence alignment analysis (Livingstone
43 C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy
44 for the Hierarchical Analysis of Residue Conservation.CABIOS Vol. 9
45 No. 6 (745-756)). See the <a href="../calculations/conservation.html">conservation calculation</a> help page for
46 a more thorough explanation of the calculation.
48 <p>For an already coloured alignment, the conservation index at each
49 alignment position is used to modify the shading intensity of the
50 colour at that position. This means that the most conserved columns
51 in each group have the most intense colours, and the least conserved
52 are the palest. The slider controls the contrast between these
54 <p>Conservation can be calculated over all sequences in an alignment, or just
55 within specific groups (such as those defined by
56 <a href="../calculations/tree.html">phylogenetic tree partitioning</a>).
57 The option 'apply to all groups' controls whether the contrast
58 slider value will be applied to the indices for the currently
59 selected group, or all groups defined over the alignment.</p>