3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
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 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/>.
18 * The Jalview Authors are detailed in the 'AUTHORS' file.
20 <head><title>Alignment Consensus Annotation</title></head>
22 <p><strong>Alignment Consensus Annotation</strong></p>
23 <p>The consensus displayed below the alignment is the percentage of the modal
24 residue per column. By default this calculation takes includes gaps in column.
25 You can choose to ignore gaps in the calculation by right clicking on the label
26 "Consensus" to the left of the consensus bar chart.
27 <p>If the modal value is shared by more than 1 residue, a "+" symbol
28 is used in the display for the simple reason that it is not possible to display
29 multiple characters in a single character space.
30 <p><strong>Copying the consensus sequence</strong></p>
31 <p>Select the <strong>"Copy Consensus Sequence"</strong> entry from
32 the consensus annotation label to copy the alignment's consensus sequence to the
35 <p><strong>Sequence logo</strong></p>
36 By clicking on the label you can also activate the sequence logo. It
37 indicates the relative amount of residues per column which can be
38 estimated by it's size in the logo. The tooltip of a column gives the
39 exact numbers for all occuring residues.
40 <br />If columns of the alignment are very diverse, then it can
41 sometimes be difficult to see the sequence logo - in this case, right
42 click on the annotation row label and select
43 <strong>Normalise Consensus Logo</strong> to scale all columns of the
44 logo to the same height.