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2 # Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
3 # Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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7 # Jalview is free software: you can redistribute it and/or
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20 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
21 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
23 * This file is part of Jalview.
25 * Jalview is free software: you can redistribute it and/or
26 * modify it under the terms of the GNU General Public License
27 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
29 * Jalview is distributed in the hope that it will be useful, but
30 * WITHOUT ANY WARRANTY; without even the implied warranty
31 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
32 * PURPOSE. See the GNU General Public License for more details.
34 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
36 <head><title>Alignment Window Menus</title></head>
39 <p><strong>Alignment Window Calculate Menu</strong></p>
41 <li><strong>Sort </strong>
43 <li><strong>by ID</strong><em><br>
44 This will sort the sequences according to sequence name. If the sort is
45 repeated, the order of the sorted sequences will be inverted. </em></li>
46 <li><strong>by Length</strong><em><br>
47 This will sort the sequences according to their length (excluding gap characters). If the sort is
48 repeated, the order of the sorted sequences will be inverted. </em></li>
49 <li><strong>by Group</strong><strong><br>
50 </strong><em>This will sort the sequences according to sequence name.
51 If the sort is repeated, the order of the sorted sequences will be inverted.
52 </em><strong></strong></li>
53 <li><strong>by Pairwise Identity<br>
54 </strong><em>This will sort the selected sequences by their percentage
55 identity to the consensus sequence. The most similar sequence is put at
57 <li><em>The <a href="../calculations/sorting.html">Sort menu</a> will have
58 some additional options if the alignment has any associated
59 score annotation, or you have just done a multiple alignment calculation
60 or opened a tree viewer window.</em><br>
64 <li><strong>Calculate Tree </strong> <br>
65 <em>Functions for calculating trees on the alignment or the currently selected
67 href="../calculations/tree.html">calculating trees</a>.</em>
69 <li><strong>Average Distance Using % Identity</strong></li>
70 <li><strong>Neighbour Joining Using % Identity</strong></li>
71 <li><strong>Average Distance Using Blosum62</strong></li>
72 <li><strong>Neighbour Joining Using Blosum62<br>
76 <li><strong>Pairwise Alignments</strong><br>
77 <em>Applies Smith and Waterman algorithm to selected sequences. See <a href="../calculations/pairwise.html">pairwise
78 alignments</a>.</em><br>
80 <li><strong>Principal Component Analysis</strong><br>
81 <em>Shows a spatial clustering of the sequences based on the BLOSUM62 scores
82 in the alignment. See <a href="../calculations/pca.html">Principal Component
83 Analysis</a>.</em> <br>
85 <li><strong>Extract Scores ... (optional)</strong><br>
86 <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>
87 When selected, these numbers are parsed into sequence associated annotation which can
88 then be used to sort the alignment via the Sort by→Score menu.</em> <br>
91 <li><strong>Autocalculate Consensus</strong><br>
92 <em>For large alignments it can be useful to deselect "Autocalculate
93 Consensus" when editing. This prevents the sometimes lengthy calculations
94 performed after each sequence edit.</em> <br>