3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
4 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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/>.
20 <title>Alignment Window Menus</title>
25 <strong>Alignment Window Calculate Menu</strong>
28 <li><strong>Sort </strong>
30 <li><strong>by ID</strong><em><br> This will sort the
31 sequences according to sequence name. If the sort is repeated, the
32 order of the sorted sequences will be inverted. </em>
34 <li><strong>by Length</strong><em><br> This will sort
35 the sequences according to their length (excluding gap
36 characters). If the sort is repeated, the order of the sorted
37 sequences will be inverted. </em>
39 <li><strong>by Group</strong><strong><br> </strong><em>This
40 will sort the sequences according to sequence name. If the sort is
41 repeated, the order of the sorted sequences will be inverted. </em><strong></strong>
43 <li><strong>by Pairwise Identity<br> </strong><em>This
44 will sort the selected sequences by their percentage identity to
45 the consensus sequence. The most similar sequence is put at the
48 <li><em>The <a href="../calculations/sorting.html">Sort
49 menu</a> will have some additional options if the alignment has any
50 associated score annotation, or you have just done a multiple
51 alignment calculation or opened a tree viewer window.</em><br></li>
53 <li><strong>Calculate Tree </strong> <br> <em>Functions
54 for calculating trees on the alignment or the currently selected
55 region. See <a href="../calculations/tree.html">calculating
58 <li><strong>Average Distance Using % Identity</strong>
60 <li><strong>Neighbour Joining Using % Identity</strong>
62 <li><strong>Average Distance Using Blosum62</strong>
64 <li><strong>Neighbour Joining Using Blosum62<br>
68 <li><strong>Pairwise Alignments</strong><br> <em>Applies
69 Smith and Waterman algorithm to selected sequences. See <a
70 href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
72 <li><strong>Principal Component Analysis</strong><br> <em>Shows
73 a spatial clustering of the sequences based on the BLOSUM62 scores
74 in the alignment. See <a href="../calculations/pca.html">Principal
75 Component Analysis</a>.</em> <br></li>
76 <li><strong>Extract Scores ... (optional)</strong><br> <em>This
77 option is only visible if Jalview detects one or more white-space
78 separated values in the description line of the alignment sequences.<br>
79 When selected, these numbers are parsed into sequence associated
80 annotation which can then be used to sort the alignment via the Sort
81 by→Score menu.</em> <br></li>
83 <li><strong>Autocalculate Consensus</strong><br> <em>For
84 large alignments it can be useful to deselect "Autocalculate
85 Consensus" when editing. This prevents the sometimes lengthy
86 calculations performed after each sequence edit.</em> <br></li>
87 <li><strong>Sort Alignment With New Tree</strong><br> <em>If
88 this option is selected, the alignment will be automatically sorted
89 whenever a new tree is calculated or loaded.</em> <br>