3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
4 * Copyright (C) 2010 J Procter, AM Waterhouse, 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>Alignment Consensus Annotation</title></head>
21 <p><strong>Alignment Consensus Annotation</strong></p>
22 <p>The consensus displayed below the alignment is the percentage of the modal
23 residue per column. By default this calculation takes includes gaps in column.
24 You can choose to ignore gaps in the calculation by right clicking on the label
25 "Consensus" to the left of the consensus bar chart.
26 <p>If the modal value is shared by more than 1 residue, a "+" symbol
27 is used in the display for the simple reason that it is not possible to display
28 multiple characters in a single character space.
29 <p><strong>Copying the consensus sequence</strong></p>
30 <p>Select the <strong>"Copy Consensus Sequence"</strong> entry from
31 the consensus annotation label to copy the alignment's consensus sequence to the