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<br>
- </strong></li>
- <li><strong>Neighbour Joining Using Sequence
- Feature Similarity</strong></li>
- <li><strong>Neighbour Joining Using Blosum62<br>
- </strong></li>
- <li><strong>Neighbour Joining Using % Identity</strong></li>
- <li><strong>Average Distance Using PAM250<br>
- </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></li>
+ <li><strong>Calculate Tree or PCA ...</strong> <br> <em>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>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 similarity scores
- calculated over 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