</strong><em>Selects all the sequences and residues in the
alignment. <br> Use <CTRL> and A (<APPLE>
and A on a MacOSX) to select all.
- </em></em></li>
+ </em></li>
<li><strong>Deselect All (Escape)<br>
</strong><em>Removes the current selection box (red dashed box) from
the alignment window. All selected sequences, residues and
Columns by Annotation</a></strong> <br /> <em>Select or Hide
columns in the alignment according to secondary structure,
labels and values shown in alignment annotation rows. </em></li>
+ <li><strong>Select Highlighted Columns</strong> <br /> <em>Selects
+ the columns currently highlighted as a result of a find, mouse
+ over, or selection event from a linked structure viewer or other
+ application. Modifiers will work on some platforms: ALT will add
+ all but the highlighted set to the column selection, and CTRL
+ (or META) will toggle the selection. </em></li>
</ul></li>
<li><strong>View</strong>
<ul>
or hide sequence features on this alignment.</em></li>
<li><strong><a
href="../features/featuresettings.html">Sequence
- Feature Settings...</a> </strong><em><br> <em>Opens the
+ Feature Settings...</a> </strong><br> <em>Opens the
Sequence Feature Settings dialog box to control the colour
and display of sequence features on the alignment, and
configure and retrieve features from DAS annotation
</strong><em>If this box is selected then the sequence names
displayed in the sequence label area will be aligned
against the left-hand edge of the alignment display,
- rather than the left-hand edge of the alignment window.
+ rather than the left-hand edge of the alignment window.</em>
</li>
<li><strong>Show Hidden Markers<br>
</strong><em>When this box is selected, positions in the
alignment where rows and columns are hidden will be
- marked by blue arrows. </li>
+ marked by blue arrows. </em></li>
<li><strong>Boxes</strong><em><br> If this is
selected the background of a residue will be coloured
using the selected background colour. Useful if used in
symbols will be rendered as a '.', highlighting
mutations in highly conserved alignments. </em></li>
- </ul></li>
</ul></li>
</ul>
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>Neighbour Joining Using PAM250 </strong></li>
- <li><strong>Neighbour Joining Using Sequence
- Feature Similarity</strong></li>
- <li><strong>Neighbour Joining Using Blosum62 </strong></li>
- <li><strong>Neighbour Joining Using % Identity</strong></li>
- <li><strong>Average Distance Using PAM250 </strong></li>
- <li><strong>Average Distance Using Sequence
- Feature Similarity</strong></li>
- <li><strong>Average Distance Using Blosum62</strong></li>
- <li><strong>Average Distance Using % Identity</strong></li>
- </ul> <strong>Note: Since Version 2.8.1, a number of
- additional similarity measures for tree calculation are
- provided in this menu.</strong></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>.
+ <li><strong>Calculate Tree or PCA ...</strong><em> <br> Opens the
+ <a href="../calculations/calculations.html">calculations dialog</a> for
+ for calculating <a href="../calculations/tree.html">trees</a> or
+ <a href="../calculations/pca.html">principle component analysis
+ plots</a> on the alignment or the currently selected
+ region.
</em><br></li>
- <li><strong>Principal Component Analysis</strong><br> <em>Shows
- a spatial clustering of the sequences based on similarity
- scores calculated with 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
+ <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>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
in Jalview 2.8.1</strong>
</li>
<li>'Standard Databases' will check sequences against
- the EBI databases plus any active DAS sequence sources<</li>
+ the EBI databases plus any active DAS sequence sources</li>
</ul> Other sub-menus allow you to pick a specific source to query
- sources are listed alphabetically according to their
nickname.