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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
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<head>
<title>Sorting Sequences</title>
</head>
<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 (Calculate->Sort):
+the use of the functions in the Sort menu (<strong>Calculate→Sort</strong>):
</p>
<ul>
-<li><strong>Sort by ID</strong>
+<li><p><strong>Sort by ID</strong></p>
<p>Orders the sequences by the alphanumeric (0-9A-Za-z)
-precedence of their names.</p>
+precedence of their names.</p><p>
</li>
-<li><strong>Sort by Group</string>
-<p>Places sequences in the same group adjacent to eachother.</p>
+<li><p><strong>Sort by Group</strong></p>
+<p>Places sequences in the same group adjacent to each other.</p><p>
</li>
-<li><strong>Sort by Pairwise Identity</strong>
+<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>
-</li><strong>Sort by Tree Order</strong>
+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 'Sort->By Tree Order->'.<p>
+alignment, its name will appear in the submenu <strong>Sort→By Tree Order</strong>.</p><p>
</li>
-<li><strong>Sort by alignment ordering</strong>
+<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 the Jalview
+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->By ..' menu.
+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