3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
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.
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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.
21 <title>Alignment Window Menus</title>
26 <strong>Alignment Window Calculate Menu</strong>
29 <li><strong>Sort </strong>
31 <li><strong>by ID</strong><em><br> This will sort the
32 sequences according to sequence name. If the sort is repeated, the
33 order of the sorted sequences will be inverted. </em>
35 <li><strong>by Length</strong><em><br> This will sort
36 the sequences according to their length (excluding gap
37 characters). If the sort is repeated, the order of the sorted
38 sequences will be inverted. </em>
40 <li><strong>by Group</strong><strong><br> </strong><em>This
41 will sort the sequences according to sequence name. If the sort is
42 repeated, the order of the sorted sequences will be inverted. </em><strong></strong>
44 <li><strong>by Pairwise Identity<br> </strong><em>This
45 will sort the selected sequences by their percentage identity to
46 the consensus sequence. The most similar sequence is put at the
49 <li><em>The <a href="../calculations/sorting.html">Sort
50 menu</a> will have some additional options if the alignment has any
51 associated score annotation, or you have just done a multiple
52 alignment calculation or opened a tree viewer window.</em><br></li>
54 <li><strong>Calculate Tree </strong> <br> <em>Functions
55 for calculating trees on the alignment or the currently selected
56 region. See <a href="../calculations/tree.html">calculating
59 <li><strong>Average Distance Using % Identity</strong>
61 <li><strong>Neighbour Joining Using % Identity</strong>
63 <li><strong>Average Distance Using Blosum62</strong>
65 <li><strong>Neighbour Joining Using Blosum62<br>
69 <li><strong>Pairwise Alignments</strong><br> <em>Applies
70 Smith and Waterman algorithm to selected sequences. See <a
71 href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
73 <li><strong>Principal Component Analysis</strong><br> <em>Shows
74 a spatial clustering of the sequences based on the BLOSUM62 scores
75 in the alignment. See <a href="../calculations/pca.html">Principal
76 Component Analysis</a>.</em> <br></li>
77 <li><strong>Extract Scores ... (optional)</strong><br> <em>This
78 option is only visible if Jalview detects one or more white-space
79 separated values in the description line of the alignment sequences.<br>
80 When selected, these numbers are parsed into sequence associated
81 annotation which can then be used to sort the alignment via the Sort
82 by→Score menu.</em> <br></li>
84 <li><strong>Autocalculate Consensus</strong><br> <em>For
85 large alignments it can be useful to deselect "Autocalculate
86 Consensus" when editing. This prevents the sometimes lengthy
87 calculations performed after each sequence edit.</em> <br></li>
88 <li><strong>Sort Alignment With New Tree</strong><br> <em>If
89 this option is selected, the alignment will be automatically sorted
90 whenever a new tree is calculated or loaded.</em> <br>