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# Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
# Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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# This file is part of Jalview.
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# 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.
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# Jalview is distributed in the hope that it will be useful, but
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# PURPOSE. See the GNU General Public License for more details.
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Alignment Conservation Annotation
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 :
Conservation is measured as a numerical index reflecting the conservation of physico-chemical properties in the alignment: Identities score highest, and the next most conserved group contain substitutions to amino acids lying in the same physico-chemical class.
Colouring an alignment by conservation
Conservation scores can be used to colour an alignment. This is
explained further in the help page for conservation colouring.