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.
13 * Jalview is distributed in the hope that it will be useful, but
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.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Alignment Window Menus</title>
28 <strong>Alignment Window Calculate Menu</strong>
31 <li><strong>Sort </strong>
33 <li><strong>by ID</strong><em><br> This will sort the
34 sequences according to sequence name. If the sort is repeated, the
35 order of the sorted sequences will be inverted. </em>
37 <li><strong>by Length</strong><em><br> This will sort
38 the sequences according to their length (excluding gap
39 characters). If the sort is repeated, the order of the sorted
40 sequences will be inverted. </em>
42 <li><strong>by Group</strong><strong><br> </strong><em>This
43 will sort the sequences according to sequence name. If the sort is
44 repeated, the order of the sorted sequences will be inverted. </em><strong></strong>
46 <li><strong>by Pairwise Identity<br> </strong><em>This
47 will sort the selected sequences by their percentage identity to
48 the consensus sequence. The most similar sequence is put at the
51 <li><em>The <a href="../calculations/sorting.html">Sort
52 menu</a> will have some additional options if the alignment has any
53 associated score annotation, or you have just done a multiple
54 alignment calculation or opened a tree viewer window.</em><br></li>
56 <li><strong>Calculate Tree </strong> <br> <em>Functions
57 for calculating trees on the alignment or the currently selected
58 region. See <a href="../calculations/tree.html">calculating
61 <li><strong>Average Distance Using % Identity</strong>
63 <li><strong>Neighbour Joining Using % Identity</strong>
65 <li><strong>Average Distance Using Blosum62</strong>
67 <li><strong>Neighbour Joining Using Blosum62<br>
71 <li><strong>Pairwise Alignments</strong><br> <em>Applies
72 Smith and Waterman algorithm to selected sequences. See <a
73 href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
75 <li><strong>Principal Component Analysis</strong><br> <em>Shows
76 a spatial clustering of the sequences based on the BLOSUM62 scores
77 in the alignment. See <a href="../calculations/pca.html">Principal
78 Component Analysis</a>.</em> <br></li>
79 <li><strong>Extract Scores ... (optional)</strong><br> <em>This
80 option is only visible if Jalview detects one or more white-space
81 separated values in the description line of the alignment sequences.<br>
82 When selected, these numbers are parsed into sequence associated
83 annotation which can then be used to sort the alignment via the Sort
84 by→Score menu.</em> <br></li>
86 <li><strong>Autocalculate Consensus</strong><br> <em>For
87 large alignments it can be useful to deselect "Autocalculate
88 Consensus" when editing. This prevents the sometimes lengthy
89 calculations performed after each sequence edit.</em> <br></li>
90 <li><strong>Sort Alignment With New Tree</strong><br> <em>If
91 this option is selected, the alignment will be automatically sorted
92 whenever a new tree is calculated or loaded.</em> <br>