</head>
<body>
<p><strong>Split Frame Views</strong></p>
-<p/></p>Coding DNA (cDNA) and its protein product can be displayed in a split view, with cDNA above and protein below. The two alignments are
-linked, with these features supported:
-<ul>
-<li>mouseover or scrolling of either alignment is followed by the other (unless you turn off <strong><a href="../menus/alwview.html">"View→Automatic Scrolling"</a></strong>)</li>
-<li>on selecting rows, columns or regions in one alignment, the corresponding selection is made in the other</li>
-<li>sequence ordering in one alignment (using the cursor, or <strong><a href="../calculate/sorting.html">"Calculate→Sort")</a></strong> is also applied to the other</li>
-<li>editing (gap insertion / deletion) in the protein alignment is reflected in the cDNA (but not vice versa)</li>
-<li>on <strong><a href="../calculations/tree.html">"Calculate Tree"</a></strong> in either alignment, grouping, colouring and sorting by tree are applied to both</li>
-<li>the <strong><a href="../menus/alwformat.html">"Format→Font"</a></strong> menu option has an option 'Scale protein residues to codons'; select this option to make each protein residue
-the same width as a DNA codon (so the alignments 'line up' vertically)</li>
-<li>menu option <strong>"View→Protein"</strong> (in the cDNA panel) or <strong>"View→Nucleotide"</strong> (in the protein panel) allows you to show or hide the complementary alignment</li>
-<li>you can adjust panel heights by dragging the divider between them using the mouse</li>
-<li>menu options <a href="menus/alwview.html"><strong>"View→New View / Expand Views / Gather Views"</strong></a> behave as for a normal alignment window, but always create new views
-as split frames</li>
-</ul>
-<p>An alignment annotation row on the protein alignment shows the <strong><a href="../calculations/consensus.html">cDNA consensus</a></strong> for each peptide column.<br/>
+ <p>
+ Jalview provides a special viewing mode to show Coding DNA (cDNA)
+ and protein product alignments as a split view, with cDNA above and
+ protein below. The two alignments are linked, allowing editing and
+ analysis to be performed at both the peptide and nucleotide level.
+ Linked protein alignments also have an additional
+ <strong>cDNA Consensus</strong> annotation row, showing the
+ distribution of codons at each column
+ of the protein alignment.
+ </p>
+ <p>
+ Split Frame views can be <a
+ href="#opensplit">created in a number of ways</a>. In the Jalview
+ Desktop, Split Frame views are saved in Jalview Projects, like any
+ other alignment view.
+ </p>
+ <p><strong>Operations supported in Split Frame Mode</strong></p>
+<p>Split Frame views allow the following:
+
+ <ul>
+ <li>Mouseover or scrolling of either alignment is followed by
+ the other (unless you turn off <strong><a
+ href="../menus/alwview.html">"View→Automatic
+ Scrolling"</a></strong>)
+ </li>
+ <li>On selecting rows, columns or regions in one alignment, the
+ corresponding selection is made in the other</li>
+ <li>Sequence ordering in one alignment (using the cursor, or <strong><a
+ href="../calculate/sorting.html">"Calculate→Sort")</a></strong> is
+ also applied to the other
+ </li>
+ <li>Editing (gap insertion / deletion) in the protein alignment
+ is reflected in the cDNA (but not vice versa)</li>
+ <li>Any trees imported or created with <strong><a
+ href="../calculations/tree.html">"Calculate Tree"</a></strong> on one of
+ the views allow both cDNA and Protein views to be grouped,
+ coloured or sorted.
+ </li>
+ <li>To allow for the different widths in cDNA and Protein
+ alignments, the <strong><a href="../menus/alwformat.html">"Format→Font"</a></strong>
+ menu option has an option 'Scale protein residues to codons'. This
+ option will make each protein residue the same width as a DNA
+ codon (so the alignments 'line up' vertically)
+ </li>
+ <li><strong>"View→Protein"</strong> (in the cDNA panel)
+ or <strong>"View→Nucleotide"</strong> (in the protein panel)
+ allows you to show or hide one or other of the linked alignment
+ panels.</li>
+ <li>Panel heights are adjusted dragging the divider between
+ them using the mouse</li>
+ <li><a href="menus/alwview.html"><strong>"View→New
+ View / Expand Views / Gather Views"</strong></a> behave as for a normal
+ alignment window, but always create new views as Split Frames</li>
+ </ul>
+ <p>An alignment annotation row on the protein alignment shows the <strong><a href="../calculations/consensus.html">cDNA consensus</a></strong> for each peptide column.<br/>
This consensus may reveal variation in nucleotides coding for conserved protein residues.</p>
-<p><strong>Opening a Split Frame View</strong></p>
+<a name="opensplit"/><p><strong>Opening a Split Frame View</strong></p>
<p>A Split Frame View can be opened in one of the following ways:</p>
<p><strong><em>Add Sequences</em></strong></p>
<p>If you add (coding) DNA sequences to an open peptide alignment, or vice versa, <em>and</em> at least one DNA sequence translates to one of the
<li>Jalview reconstructs the alignment of its complement (in
this case, cDNA) by inserting gaps in the corresponding positions</li>
</ul>
- <p><strong>Reconstructed Alignments</strong>
- Reconstructed alignments are typically <em>not</em>
- the same as the alignment produced by aligning the complement
- sequence set directly with the external service. However, in the
- case of protein alignments, a reconstructed cDNA alignment is often
- more reliable than one calculated without coding information.
- Reconstructed cDNA alignments are also more informative than the
- original protein alignment when calculating phylogenetic trees or
- performing other kinds of molecular evolution analysis.
+ <p>
+ <a name="reconalignment" /><strong>Reconstructed Alignments</strong>
+ </p>
+ <p>
+ Reconstructed alignments are typically <em>not</em> the same as the
+ alignment produced by aligning the complement sequence set directly
+ with the external service. However, in the case of protein
+ alignments, a reconstructed cDNA alignment is often more reliable
+ than one calculated without coding information. Reconstructed cDNA
+ alignments are also more informative than the original protein
+ alignment when calculating phylogenetic trees or performing other
+ kinds of molecular evolution analysis.
</p>
<p>
<em>Split Frame Views were introduced in Jalview 2.9</em>
git://source.jalview.org / jalview.git / blobdiff