--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Split Frame Views</title>
+</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>
+</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>
+<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
+peptide sequences, then the option to open in a split window is offered. The DNA may include start and/or stop codons, but no non-coding (intron)
+sequence.</p>
+
+<p>This option is available in Jalview Desktop (when adding sequences by any supported method), and Jalview applet (adding from textbox).
+The additional options below apply to Jalview Desktop only.</p>
+
+<p><strong><em>Translate as cDNA</em></strong></p>
+<p>Menu option <strong><a href="../menus/alwcalculate.html">"Calculate | Translate as cDNA"</a></strong> is available for a nucleotide alignment. Selecting this option shows the DNA and its
+calculated protein product in a Split Frame view.</p>
+
+<p><strong><em>Get Cross-References</em></strong></p>
+<p>Menu option <strong><a href="../menus/alwcalculate.html">"Calculate | Get Cross-References"</a></strong> is available for fetched sequences which have cross-references to other databases.
+On selecting protein cross-references (for a cDNA alignment), or DNA xrefs (for peptide), a Split Frame view is opened showing cDNA and peptide.</p>
+
+<p><strong><em>Realign Split View</em></strong></p>
+<p>If you invoke a web service to realign either half of a Split Frame, then the resulting realignment is displayed in a new
+Split Frame.</p>
+<ul>
+<li>the alignment you chose to realign (for example, peptide) is displayed as aligned by the external web service</li>
+<li>Jalview 'aligns' its complement (in this case, cDNA) similarly, by inserting corresponding gaps
+ <ul>
+ <li>NB this is <em>not</em> the same as aligning the complement using the external service, which may give different results</li>
+ </ul>
+</li>
+</ul>
+
+
+<p><em>Split Frame Views were introduced in Jalview 2.?.?</em></p>
+</body>
+</html>
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>Translate as cDNA</strong> (not applet)<br><em>This option is visible for nucleotide alignments.
+ Selecting this option shows the DNA's calculated protein product in a new 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.</em> <br></li>
+ <li><strong>Get Cross-References</strong> (not applet)<br><em>This option is visible where sequences have cross-references to
+ other standard databases; for example, an EMBL entry may have cross-references to one or more UNIPROT entries.
+ Select the database to view all cross-referenced sequences in a new window.</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
git://source.jalview.org / jalview.git / commitdiff