<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.
*
*
* 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>
+ <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