<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
* 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 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>
+</ul>
+ </body>
+</html>
git://source.jalview.org / jalview.git / blobdiff