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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
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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 (<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>
+ <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