3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
4 * Copyright (C) 2010 J Procter, AM Waterhouse, 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/>.
19 <head><title>Alignment Window Menus</title></head>
22 <p><strong>Alignment Window Calculate Menu</strong></p>
24 <li><strong>Sort </strong>
26 <li><strong>by ID</strong><em><br>
27 This will sort the sequences according to sequence name. If the sort is
28 repeated, the order of the sorted sequences will be inverted. </em></li>
29 <li><strong>by Length</strong><em><br>
30 This will sort the sequences according to their length (excluding gap characters). If the sort is
31 repeated, the order of the sorted sequences will be inverted. </em></li>
32 <li><strong>by Group</strong><strong><br>
33 </strong><em>This will sort the sequences according to sequence name.
34 If the sort is repeated, the order of the sorted sequences will be inverted.
35 </em><strong></strong></li>
36 <li><strong>by Pairwise Identity<br>
37 </strong><em>This will sort the selected sequences by their percentage
38 identity to the consensus sequence. The most similar sequence is put at
40 <li><em>The <a href="../calculations/sorting.html">Sort menu</a> will have
41 some additional options if the alignment has any associated
42 score annotation, or you have just done a multiple alignment calculation
43 or opened a tree viewer window.</em><br>
47 <li><strong>Calculate Tree </strong> <br>
48 <em>Functions for calculating trees on the alignment or the currently selected
50 href="../calculations/tree.html">calculating trees</a>.</em>
52 <li><strong>Average Distance Using % Identity</strong></li>
53 <li><strong>Neighbour Joining Using % Identity</strong></li>
54 <li><strong>Average Distance Using Blosum62</strong></li>
55 <li><strong>Neighbour Joining Using Blosum62<br>
59 <li><strong>Pairwise Alignments</strong><br>
60 <em>Applies Smith and Waterman algorithm to selected sequences. See <a href="../calculations/pairwise.html">pairwise
61 alignments</a>.</em><br>
63 <li><strong>Principal Component Analysis</strong><br>
64 <em>Shows a spatial clustering of the sequences based on the BLOSUM62 scores
65 in the alignment. See <a href="../calculations/pca.html">Principal Component
66 Analysis</a>.</em> <br>
68 <li><strong>Extract Scores ... (optional)</strong><br>
69 <em>This option is only visible if Jalview detects one or more white-space separated values in the description line of the alignment sequences.<br>
70 When selected, these numbers are parsed into sequence associated annotation which can
71 then be used to sort the alignment via the Sort by→Score menu.</em> <br>
74 <li><strong>Autocalculate Consensus</strong><br>
75 <em>For large alignments it can be useful to deselect "Autocalculate
76 Consensus" when editing. This prevents the sometimes lengthy calculations
77 performed after each sequence edit.</em> <br>