<html>
-<head><title>Alignment Window Menus</title></head>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+-->
+<head>
+<title>Alignment Window Menus</title>
+</head>
<body>
-<p><strong>Alignment Window Calculate Menu</strong></p>
-<ul>
- <li><strong>Sort </strong>
- <ul>
- <li><strong>by ID</strong><em><br>
- This will sort the sequences according to sequence name. If the sort is
- repeated, the order of the sorted sequences will be inverted. </em></li>
- <li><strong>by Group</strong><strong><br>
- </strong><em>This will sort the sequences according to sequence name.
- If the sort is repeated, the order of the sorted sequences will be inverted.
- </em><strong></strong></li>
- <li><strong>by Pairwise Identity<br>
- </strong><em>This will sort the selected sequences by their percentage
- identity to the consensus sequence. The most similar sequence is put at
- the top. </em></li>
- <li><em>The <a href="../calculations/sorting.html">Sort menu</a> will have
- some additional options if you have just done a multiple alignment calculation,
- or opened a tree viewer window.</em><br>
- </li>
- </ul>
- </li>
- <li><strong>Calculate Tree </strong> <br>
- <em>Functions for calculating trees on the alignment or the currently selected
- region. See <a
- href="../calculations/tree.html">calculating trees</a>.</em>
- <ul>
- <li><strong>Average Distance Using % Identity</strong></li>
- <li><strong>Neighbour Joining Using % Identity</strong></li>
- <li><strong>Average Distance Using Blosum62</strong></li>
- <li><strong>Neighbour Joining Using Blosum62<br>
- </strong></li>
- </ul>
- </li>
- <li><strong>Pairwise Alignments</strong><br>
- <em>Applies Smith and Waterman algorithm to selected sequences. See <a href="../calculations/pairwise.html">pairwise
- alignments</a>.</em><br>
- </li>
- <li><strong>Principal Component Analysis</strong><br>
- <em>Shows a spatial clustering of the sequences based on the BLOSUM62 scores
- in the alignment. See <a href="../calculations/pca.html">Principal Component
- Analysis</a>.</em> <br>
- </li>
- <li><strong>Autocalculate Consensus</strong><br>
- <em>For large alignments it can be useful to deselect "Autocalculate
- Consensus" when editing. This prevents the sometimes lengthy calculations
- performed after each sequence edit.</em> <br>
- </li>
-</ul>
- </body>
+ <p>
+ <strong>Alignment Window Calculate Menu</strong>
+ </p>
+ <ul>
+ <li><strong>Sort </strong>
+ <ul>
+ <li><strong>by ID</strong><em><br> This will sort the
+ sequences according to sequence name. If the sort is repeated, the
+ order of the sorted sequences will be inverted. </em>
+ </li>
+ <li><strong>by Length</strong><em><br> This will sort
+ the sequences according to their length (excluding gap
+ characters). If the sort is repeated, the order of the sorted
+ sequences will be inverted. </em>
+ </li>
+ <li><strong>by Group</strong><strong><br> </strong><em>This
+ will sort the sequences according to sequence name. If the sort is
+ repeated, the order of the sorted sequences will be inverted. </em><strong></strong>
+ </li>
+ <li><strong>by Pairwise Identity<br> </strong><em>This
+ will sort the selected sequences by their percentage identity to
+ the consensus sequence. The most similar sequence is put at the
+ top. </em>
+ </li>
+ <li><em>The <a href="../calculations/sorting.html">Sort
+ menu</a> will have some additional options if the alignment has any
+ associated score annotation, or you have just done a multiple
+ alignment calculation or opened a tree viewer window.</em><br></li>
+ </ul></li>
+ <li><strong>Calculate Tree </strong> <br> <em>Functions
+ for calculating trees on the alignment or the currently selected
+ region. See <a href="../calculations/tree.html">calculating
+ trees</a>.</em>
+ <ul>
+ <li><strong>Average Distance Using % Identity</strong>
+ </li>
+ <li><strong>Neighbour Joining Using % Identity</strong>
+ </li>
+ <li><strong>Average Distance Using Blosum62</strong>
+ </li>
+ <li><strong>Neighbour Joining Using Blosum62<br>
+ </strong>
+ </li>
+ </ul></li>
+ <li><strong>Pairwise Alignments</strong><br> <em>Applies
+ Smith and Waterman algorithm to selected sequences. See <a
+ href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
+ </li>
+ <li><strong>Principal Component Analysis</strong><br> <em>Shows
+ a spatial clustering of the sequences based on the BLOSUM62 scores
+ in the alignment. See <a href="../calculations/pca.html">Principal
+ Component Analysis</a>.</em> <br></li>
+ <li><strong>Extract Scores ... (optional)</strong><br> <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>
+ When selected, these numbers are parsed into sequence associated
+ annotation which can then be used to sort the alignment via the Sort
+ by→Score menu.</em> <br></li>
+
+ <li><strong>Autocalculate Consensus</strong><br> <em>For
+ large alignments it can be useful to deselect "Autocalculate
+ Consensus" when editing. This prevents the sometimes lengthy
+ calculations performed after each sequence edit.</em> <br></li>
+ <li><strong>Sort Alignment With New Tree</strong><br> <em>If
+ this option is selected, the alignment will be automatically sorted
+ whenever a new tree is calculated or loaded.</em> <br>
+ </li>
+ </ul>
+</body>
</html>
git://source.jalview.org / jalview.git / blobdiff