3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
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/>.
20 <title>Removing Redundancy</title>
23 <p><strong>Removing redundancy</strong></p>
24 <p>Selecting the option in the Alignment window's <strong>Edit</strong>
25 menu or pressing <strong>'CONTROL+D'</strong> brings up a dialog box
26 asking you to select a threshold. If the percentage identity between the
27 aligned positions of any two sequences in the visible alignment exceeds
28 this value, the shorter sequence is discarded.<br><em>Note:</em> The redundancy
29 calculation is done when the dialog box is opened. For large numbers
30 of sequences this can take a long time as all pairs have to be compared.