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<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 (Calculate->Sort):
-</p>
-<ul>
-<li><strong>Sort by ID</strong>
-<p>Orders the sequences by the alphanumeric (0-9A-Za-z)
-precedence of their names.</p>
-</li>
-<li><strong>Sort by Group</string>
-<p>Places sequences in the same group adjacent to eachother.</p>
-</li>
-<li><strong>Sort by Pairwise Identity</strong>
-<p>Places pairs of sequences together that align with the greatest
-fraction of conserved residues.
-</p>
-</li><strong>Sort by Tree Order</strong>
-<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>
-</li>
-<li><strong>Sort by alignment ordering</strong>
-<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
-alignment web services, the alignment ordering can be recovered by
-its corresponding entry in the 'Sort->By ..' menu.
-</p>
-</li>
-</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>
+ <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>Sorts sequences in the selection or alignment according to percent identity with respect to the first sequence in the view.</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>Sorting according to sequence features</strong><br />
+ Additional sort operations for alignments containing sequence
+ features are provided in the <strong><a
+ href="../features/featuresettings.html#sortbyfeature">Feature
+ Settings</a></strong> dialog, opened via <strong>View→Feature
+ Settings...</strong>
+ <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 both cases, for sequences which are equivalent under the
+ sort operation, their order will be preserved (since version 2.10).
+ 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>