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<!--
- * 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, 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>Sorting Sequences</title>
+</head>
+<body>
+<p><strong>Sorting Sequences</strong></p>
+<p>Any group of selected sequences may be reordered by pressing the
+up or down arrow keys. The whole alignment may also be reordered by
+the use of the functions in the Sort menu (<strong>Calculate→Sort</strong>):
+</p>
+<ul>
+<li><p><strong>Sort by ID</strong></p>
+<p>Orders the sequences by the alphanumeric (0-9A-Za-z)
+precedence of their names.</p><p>
+</li>
+<li><p><strong>Sort by Group</strong></p>
+<p>Places sequences in the same group adjacent to each other.</p><p>
+</li>
+<li><p><strong>Sort by Pairwise Identity</strong></p>
+<p>Places pairs of sequences together that align with the greatest
+fraction of conserved residues.
+</p><p>
+</li>
+<li><p><strong>Sort by Tree Order</strong></p>
+<p>The leaf ordering of a particular phylogenetic tree is used to
+order the sequences corresponding to those leaves in the
+alignment.<br>
+If a tree has been calculated from or associated with the current
+alignment, its name will appear in the submenu <strong>Sort→By Tree Order</strong>.</p><p>
+</li>
+<li><p><strong>Sort by alignment ordering</strong></p>
+<p>Multiple alignment methods often order the sequences in their
+alignments by some measure of sequence identity.<br>
+If the current alignment has been generated by one of Jalview's
+alignment web services, the alignment ordering can be recovered by
+its corresponding entry in the Sort menu.
+</p>
+</li>
+<li><p><strong>Sort by Score</strong></p>
+<p>This menu appears if the alignment contains any <a href="../features/annotationsFormat.html">sequence associated
+alignment annotation</a> with associated score values. Each entry is the
+label for a distinct group of sequence associated annotation
+scores which can be used for sorting.</p>
+</ul>
+<p><strong>Reversing the Order</strong></p>
+<p>Selecting any item from the Sort menu will sort sequences in an
+ascending order according to the property defining the sort. If the
+same sort is re-applied, the sequences will be sorted in the inverse
+order. In the case of trees and alignment orderings, Jalview will
+remember your last choice for sorting the alignment and only apply the
+inverse ordering if you select the same tree or alignment ordering
+item again.</p>
+
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff