<html>
-<head><title>Alignment Window Menus</title></head>
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+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<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 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>
+ <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>Translate as cDNA</strong> (not applet)<br><em>This option is visible for nucleotide alignments.
+ Selecting this option shows the DNA's calculated protein product in a new <a href="../features/splitView.html">split frame</a> window. Note that the
+ translation is not frame- or intron-aware; it simply translates all codons in each sequence, using the
+ standard <a href="../misc/geneticCode.html">genetic code</a> (any incomplete final codon is discarded).
+ You can perform this action on the whole alignment,
+ or selected rows, columns, or regions.</em> <br></li>
+ <li><strong>Get Cross-References</strong> (not applet)<br><em>This option is visible where sequences have cross-references to
+ other standard databases; for example, an EMBL entry may have cross-references to one or more UNIPROT entries.
+ Select the database to view all cross-referenced sequences in a new <a href="../features/splitView.html">split frame</a> window.</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>
+ <li><strong>Sort Alignment With New Tree</strong><br> <em>If
+ this option is selected, the alignment will be automatically sorted
+ whenever a new tree is calculated or loaded.</em> <br>
+ </li>
+ </ul>
+</body>
</html>