</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 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: SHIFT will
- add columns to selection, ALT will invert the highlighted set
- before selection, and CTRL (or META) will toggle the selection.
- </em></li>
+ 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.
<ul>
<li><strong>JPred Secondary Structure Prediction</strong><br>
<em>Secondary structure prediction by network
- consensus. See the <a href="../webServices/jnet.html">Jpred3</a>
+ consensus. See the <a href="../webServices/jnet.html">Jpred</a>
client entry for more information. The behaviour of this
calculation depends on the current selection:
<ul>
<li>If nothing is selected, and the displayed
- sequences appear to be aligned, then a JNet prediction
+ sequences appear to be aligned, then a JPred prediction
will be run for the first sequence in the alignment,
using the current alignment. Otherwise the first
sequence will be submitted for prediction.</li>
<li>If just one sequence (or a region on one
sequence) has been selected, it will be submitted to
- the automatic JNet prediction server for homolog
+ the automatic JPred prediction server for homolog
detection and prediction.</li>
<li>If a set of sequences are selected, and they
appear to be aligned, then the alignment will be used
- for a Jnet prediction on the <strong>first</strong>
+ for a JPred prediction on the <strong>first</strong>
sequence in the set (that is, the one that appears
first in the alignment window).
</li>