3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
4 * Copyright (C) 2014 The Jalview Authors
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
11 * of the License, or (at your option) any later version.
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14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
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20 * The Jalview Authors are detailed in the 'AUTHORS' file.
22 <head><title>Alignment Consensus Annotation</title></head>
24 <p><strong>Alignment Consensus Annotation</strong></p>
25 <p>The consensus displayed below the alignment is the percentage of the modal
26 residue per column. By default this calculation includes gaps in columns.
27 You can choose to ignore gaps in the calculation by right clicking on the label
28 "Consensus" to the left of the consensus bar chart.
29 <p>If the modal value is shared by more than 1 residue, a "+" symbol
30 is used in the display for the simple reason that it is not possible to display
31 multiple characters in a single character space.
32 <p><strong>Copying the consensus sequence</strong></p>
33 <p>Select the <strong>"Copy Consensus Sequence"</strong> entry from
34 the consensus annotation label to copy the alignment's consensus sequence to the
37 <p><strong>Sequence logo</strong></p>
38 By clicking on the label you can also activate the sequence logo. It
39 indicates the relative amount of residues per column which can be
40 estimated by its size in the logo. The tooltip of a column gives the
41 exact numbers for all occurring residues.
42 <br />If columns of the alignment are very diverse, then it can
43 sometimes be difficult to see the sequence logo - in this case, right
44 click on the annotation row label and select
45 <strong>Normalise Consensus Logo</strong> to scale all columns of the
46 logo to the same height.