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23 <title>Sorting Sequences</title>
27 <strong>Sorting Sequences</strong>
30 Any group of selected sequences may be reordered by pressing the up
31 or down arrow keys. The whole alignment may also be reordered by the
32 use of the functions in the Sort menu (<strong>Calculate→Sort</strong>):
36 <strong>Sort by ID</strong>
38 <p>Orders the sequences by the alphanumeric (0-9A-Za-z)
39 precedence of their names.</p>
42 <strong>Sort by Group</strong>
44 <p>Places sequences in the same group adjacent to each other.</p>
47 <strong>Sort by Pairwise Identity</strong>
49 <p>Sorts sequences in the selection or alignment according to percent identity with respect to the first sequence in the view.</p>
52 <strong>Sort by Tree Order</strong>
55 The leaf ordering of a particular phylogenetic tree is used to
56 order the sequences corresponding to those leaves in the
57 alignment.<br> If a tree has been calculated from or
58 associated with the current alignment, its name will appear in
59 the submenu <strong>Sort→By Tree Order</strong>.
63 <strong>Sort by alignment ordering</strong>
66 Multiple alignment methods often order the sequences in their
67 alignments by some measure of sequence identity.<br> If the
68 current alignment has been generated by one of Jalview's
69 alignment web services, the alignment ordering can be recovered
70 by its corresponding entry in the Sort menu.
73 <strong>Sort by Score</strong>
76 This menu appears if the alignment contains any <a
77 href="../features/annotationsFormat.html">sequence
78 associated alignment annotation</a> with associated score values.
79 Each entry is the label for a distinct group of sequence
80 associated annotation scores which can be used for sorting.
84 <strong>Sorting according to sequence features</strong><br />
85 Additional sort operations for alignments containing sequence
86 features are provided in the <strong><a
87 href="../features/featuresettings.html#sortbyfeature">Feature
88 Settings</a></strong> dialog, opened via <strong>View→Feature
91 <strong>Reversing the Order</strong>
93 <p>Selecting any item from the Sort menu will sort sequences in an
94 ascending order according to the property defining the sort. If the
95 same sort is re-applied, the sequences will be sorted in the inverse
96 order. In both cases, for sequences which are equivalent under the
97 sort operation, their order will be preserved (since version 2.10).
98 In the case of trees and alignment orderings, Jalview will remember
99 your last choice for sorting the alignment and only apply the
100 inverse ordering if you select the same tree or alignment ordering