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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>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>
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