#------------------------------------------------------------------------------- # Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1) # Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle # # 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 . #------------------------------------------------------------------------------- Alignment Conservation Annotation

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.