* 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/>.
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-<head><title>Alignment Window Menus</title></head>
-
-<body>
-<p><strong>Alignment Window Calculate Menu</strong></p>
-<ul>
- <li><strong>Sort </strong>
- <ul>
- <li><strong>by ID</strong><em><br>
- This will sort the sequences according to sequence name. If the sort is
- repeated, the order of the sorted sequences will be inverted. </em></li>
- <li><strong>by Length</strong><em><br>
- This will sort the sequences according to their length (excluding gap characters). If the sort is
- repeated, the order of the sorted sequences will be inverted. </em></li>
- <li><strong>by Group</strong><strong><br>
- </strong><em>This will sort the sequences according to sequence name.
- If the sort is repeated, the order of the sorted sequences will be inverted.
- </em><strong></strong></li>
- <li><strong>by Pairwise Identity<br>
- </strong><em>This will sort the selected sequences by their percentage
- identity to the consensus sequence. The most similar sequence is put at
- the top. </em></li>
- <li><em>The <a href="../calculations/sorting.html">Sort menu</a> will have
- some additional options if the alignment has any associated
- score annotation, or you have just done a multiple alignment calculation
- or opened a tree viewer window.</em><br>
- </li>
- </ul>
- </li>
- <li><strong>Calculate Tree </strong> <br>
- <em>Functions for calculating trees on the alignment or the currently selected
- region. See <a
- href="../calculations/tree.html">calculating trees</a>.</em>
- <ul>
- <li><strong>Average Distance Using % Identity</strong></li>
- <li><strong>Neighbour Joining Using % Identity</strong></li>
- <li><strong>Average Distance Using Blosum62</strong></li>
- <li><strong>Neighbour Joining Using Blosum62<br>
- </strong></li>
- </ul>
- </li>
- <li><strong>Pairwise Alignments</strong><br>
- <em>Applies Smith and Waterman algorithm to selected sequences. See <a href="../calculations/pairwise.html">pairwise
- alignments</a>.</em><br>
- </li>
- <li><strong>Principal Component Analysis</strong><br>
- <em>Shows a spatial clustering of the sequences based on the BLOSUM62 scores
- in the alignment. See <a href="../calculations/pca.html">Principal Component
- Analysis</a>.</em> <br>
- </li>
- <li><strong>Extract Scores ... (optional)</strong><br>
- <em>This option is only visible if Jalview detects one or more white-space separated values in the description line of the alignment sequences.<br>
- When selected, these numbers are parsed into sequence associated annotation which can
- then be used to sort the alignment via the Sort by→Score menu.</em> <br>
- </li>
-
- <li><strong>Autocalculate Consensus</strong><br>
- <em>For large alignments it can be useful to deselect "Autocalculate
- Consensus" when editing. This prevents the sometimes lengthy calculations
- performed after each sequence edit.</em> <br>
- </li>
-</ul>
- </body>
-</html>
+-->