* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
---!>
-<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>
-
-</body>
-</html>
+-->
git://source.jalview.org / jalview.git / blobdiff