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
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
+ <li><strong>Translate as cDNA</strong><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.
+ translates all codons in each sequence. You can use the standard <a
+ href="../misc/geneticCode.html">genetic code</a>, or choose an
+ alternative code table (any incomplete final codon is discarded).
+ You can perform this action on the whole alignment, or selected
+ rows, columns, or regions. Alternative code tables were added in
+ Jalview 2.11.
</em> <br></li>
<li><strong>Reverse, Reverse Complement</strong> (not applet)<br>
<em>These options are visible for nucleotide alignments.