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2 # Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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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/>.
37 <title>Removing Redundancy</title>
40 <p><strong>Removing redundancy</strong></p>
41 <p>Selecting the option in the Alignment window's <strong>Edit</strong>
42 menu or pressing <strong>'CONTROL+D'</strong> brings up a dialog box
43 asking you to select a threshold. If the percentage identity between the
44 aligned positions of any two sequences in the visible alignment exceeds
45 this value, the shorter sequence is discarded.<br><em>Note:</em> The redundancy
46 calculation is done when the dialog box is opened. For large numbers
47 of sequences this can take a long time as all pairs have to be compared.