X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=5f60ba52d6323b95055ab6742350fe4fc583404d;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=7102fd740ba47d30f6b6ea14f736d070e0b5b62f;hpb=de255c8c87707a2cd2a2a15f5ad04ed10fe5846d;p=jalview.git

diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index 7102fd7..5f60ba5 100755
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -29,483 +29,519 @@
     <strong>Alignment Window Menus</strong>
   </p>
   <ul>
-		<li><strong>File</strong>
-			<ul>
-				<li><strong>Fetch Sequence</strong><br> <em>Shows a
-						dialog window in which you can retrieve known ids from Uniprot,
-						EMBL, EMBLCDS, PFAM, Rfam, or PDB database using Web Services provided by the
-						European Bioinformatics Institute. See <a
-						href="../features/seqfetch.html">Sequence Fetcher</a> </em>.</li>
-				<li><strong>Add Sequences</strong><em><br> Add
-						sequences to the visible alignment from file, URL, or cut &amp;
-						paste window </em>
-				</li>
-				<li><strong>Reload</strong><em><br> Reloads the
-						alignment from the original file, if available.<br> <strong>Warning:
-							This will delete any edits, analyses and colourings applied since
-							the alignment was last saved, and cannot be undone.</strong> </em>
-				</li>
-				<li><strong>Save (Control S)</strong><em><br> Saves
-						the alignment to the file it was loaded from (if available), in
-						the same format, updating the original in place. </em>
-				</li>
-				<li><strong>Save As (Control Shift S)<br> </strong><em>Save
-						the alignment to local file. A file selection window will open,
-						use the &quot;Files of type:&quot; selection box to determine
-						which <a href="../io/index.html">alignment format</a> to save as.</em>
-				</li>
-				<li><strong>Output to Textbox<br> </strong><em>The
-						alignment will be displayed in plain text in a new window, which
-						you can &quot;Copy and Paste&quot; using the pull down menu, or
-						your standard operating system copy and paste keys. The output
-						window also has a <strong>&quot;New Window&quot;</strong> button
-						to import the (possibly edited) text as a new alignment.<br>
-						Select the format of the text by selecting one of the following
-						menu items.</em>
-					<ul>
-						<li><strong>FASTA</strong> </li>
-						<li><strong>MSF</strong></li>
-						<li><strong>CLUSTAL</strong></li>
-						<li><strong>BLC</strong></li>
-						<li><strong>PIR</strong></li>
-						<li><strong>PFAM</strong></li>
-						<li><strong>PileUp</strong></li>
-						<li><strong>AMSA</strong></li>
-						<li><strong>STH</strong></li>
-						<li><strong>Phylip</strong></li>
-						<li><strong>JSON</strong></li>
-					</ul></li>
-<li><strong>Page Setup ...</strong><br>
-	<em>Open the printing system's Page Setup dialog box, to
-	control page size, layout and orientation.</em></li>
-	<li><strong>Print (Control P)<br>
-	</strong><em>Jalview will print the alignment using the current fonts and
-	colours of your alignment. If the alignment has annotations visible,
-	these will be printed below the alignment. If the alignment is wrapped
-	the number of residues per line of your alignment will depend on the
-	paper width or your alignment window width, whichever is the smaller. </em></li>
-	<li><strong>Export Image</strong> <em><br>
-	Creates an alignment graphic with the current view's annotation,
-	alignment background colours and group colours. If the alignment is <a
-		href="../features/wrap.html">wrapped</a>, the output will also be
-	wrapped and will have the same visible residue width as the open
-	alignment. </em>
-	<ul>
-		<li><strong>HTML<br>
-		</strong><em>Create a <a href="../io/export.html">web page</a> from your
-		alignment.</em></li>
-		<li><strong>EPS<br>
-		</strong><em>Create an <a href="../io/export.html">Encapsulated
-		Postscript</a> file from your alignment.</em></li>
-		<li><strong>PNG<br>
-		</strong><em>Create a <a href="../io/export.html">Portable Network
-		Graphics</a> file from your alignment.</em></li>
-		<li><strong>SVG<br>
-		</strong><em>Create a <a href="../io/export.html">Scalable Vector Graphics</a> file from your alignment for embedding in web pages.</em></li>
-		<li><strong>BioJS<br>
-		</strong><em>Create a <a href="../io/export.html">BioJS MSA Viewer HTML </a> file from your alignment.</em></li>
-	</ul>
-	</li>
+    <li><strong>File</strong>
+      <ul>
+        <li><strong>Fetch Sequence</strong><br> <em>Shows
+            a dialog window in which you can retrieve known ids from
+            Uniprot, EMBL, EMBLCDS, PFAM, Rfam, or PDB database using
+            Web Services provided by the European Bioinformatics
+            Institute. See <a href="../features/seqfetch.html">Sequence
+              Fetcher</a>
+        </em>.</li>
+        <li><strong>Add Sequences</strong><em><br> Add
+            sequences to the visible alignment from file, URL, or cut
+            &amp; paste window </em></li>
+        <li><strong>Reload</strong><em><br> Reloads the
+            alignment from the original file, if available.<br> <strong>Warning:
+              This will delete any edits, analyses and colourings
+              applied since the alignment was last saved, and cannot be
+              undone.</strong> </em></li>
+        <li><strong>Save (Control S)</strong><em><br>
+            Saves the alignment to the file it was loaded from (if
+            available), in the same format, updating the original in
+            place. </em></li>
+        <li><strong>Save As (Control Shift S)<br>
+        </strong><em>Save the alignment to local file. A file selection
+            window will open, use the &quot;Files of type:&quot;
+            selection box to determine which <a href="../io/index.html">alignment
+              format</a> to save as.
+        </em></li>
+        <li><strong>Output to Textbox<br>
+        </strong><em>The alignment will be displayed in plain text in a new
+            window, which you can &quot;Copy and Paste&quot; using the
+            pull down menu, or your standard operating system copy and
+            paste keys. The output window also has a <strong>&quot;New
+              Window&quot;</strong> button to import the (possibly edited) text
+            as a new alignment.<br> Select the format of the text
+            by selecting one of the following menu items.
+        </em>
+          <ul>
+            <li><strong>FASTA</strong></li>
+            <li><strong>MSF</strong></li>
+            <li><strong>CLUSTAL</strong></li>
+            <li><strong>BLC</strong></li>
+            <li><strong>PIR</strong></li>
+            <li><strong>PFAM</strong></li>
+            <li><strong>PileUp</strong></li>
+            <li><strong>AMSA</strong></li>
+            <li><strong>STH</strong></li>
+            <li><strong>Phylip</strong></li>
+            <li><strong>JSON</strong></li>
+          </ul></li>
+        <li><strong>Page Setup ...</strong><br> <em>Open
+            the printing system's Page Setup dialog box, to control page
+            size, layout and orientation.</em></li>
+        <li><strong>Print (Control P)<br>
+        </strong><em>Jalview will print the alignment using the current
+            fonts and colours of your alignment. If the alignment has
+            annotations visible, these will be printed below the
+            alignment. If the alignment is wrapped the number of
+            residues per line of your alignment will depend on the paper
+            width or your alignment window width, whichever is the
+            smaller. </em></li>
+        <li><strong>Export Image</strong> <em><br>
+            Creates an alignment graphic with the current view's
+            annotation, alignment background colours and group colours.
+            If the alignment is <a href="../features/wrap.html">wrapped</a>,
+            the output will also be wrapped and will have the same
+            visible residue width as the open alignment. </em>
+          <ul>
+            <li><strong>HTML<br>
+            </strong><em>Create a <a href="../io/export.html">web page</a>
+                from your alignment.
+            </em></li>
+            <li><strong>EPS<br>
+            </strong><em>Create an <a href="../io/export.html">Encapsulated
+                  Postscript</a> file from your alignment.
+            </em></li>
+            <li><strong>PNG<br>
+            </strong><em>Create a <a href="../io/export.html">Portable
+                  Network Graphics</a> file from your alignment.
+            </em></li>
+            <li><strong>SVG<br>
+            </strong><em>Create a <a href="../io/export.html">Scalable
+                  Vector Graphics</a> file from your alignment for embedding
+                in web pages.
+            </em></li>
+            <li><strong>BioJS<br>
+            </strong><em>Create a <a href="../io/export.html">BioJS MSA
+                  Viewer HTML </a> file from your alignment.
+            </em></li>
+          </ul></li>
         <li><strong>Export Features</strong><em><br> All
-						features visible on the alignment can be saved to file or
-						displayed in a textbox in either Jalview or GFF format</em>
-				</li>
-				<li><strong>Export Annotations</strong><em><br> All
-						annotations visible on the alignment can be saved to file or
-						displayed in a textbox in Jalview annotations format. </em>
-				</li>
-				<li><strong>Load Associated Tree<br> </strong><em>Jalview
-						can <a href="../calculations/treeviewer.html">view trees</a>
-						 stored in the Newick file format, and associate them with the
-						alignment. Note: the ids of the tree file and your alignment MUST
-						be the same.</em></li>
-				<li><strong>Load Features / Annotations<br> </strong><em>Load
-						files describing precalculated <a
-						href="../features/featuresFormat.html">sequence features</a> or <a
-						href="../features/annotationsFormat.html">alignment
-							annotations</a>.</em></li>
-				<li><strong>Close (Control W)</strong><br> <em>Close
-						the alignment window. Make sure you have saved your alignment
-						before you close - either from the Desktop's <strong>Save Project</strong> File menu option, or by using the <strong>Save
-							As</strong> menu.</em>
-				</li>
-			</ul></li>
-		<li><strong>Edit</strong>
-			<ul>
-				<li><strong>Undo (Control Z)</strong><em><br> This
-						will undo any edits you make to the alignment. This applies to
-						insertion or deletion of gaps, cutting residues or sequences from
-						the alignment or pasting sequences to the current alignment or
-						sorting the alignment. <strong>NOTE:</strong> It DOES NOT undo
-						colour changes, adjustments to group sizes, or changes to the
-						annotation panel. </em>
-				</li>
-				<li><strong>Redo (Control Y)<br> </strong><em>Any
-						actions which you undo can be redone using redo. </em>
-				</li>
-				<li><strong>Cut (Control X)<br> </strong><em>This
-						will make a copy of the currently selected residues before
-						removing them from your alignment. Click on a sequence name if you
-						wish to select a whole sequence. <br> Use &lt;CTRL&gt; and X
-						(&lt;APPLE&gt; and X on MacOSX) to cut.</em>
-				</li>
-				<li><strong>Copy (Control C)</strong><br> <em>Copies
-						the currently selected residues to the system clipboard - you can
-						also do this by pressing &lt;CTRL&gt; and C (&lt;APPLE&gt; and C
-						on MacOSX). <br> If you try to paste the clipboard contents
-						to a text editor, you will see the format of the copied residues
-						FASTA.</em></li>
-				<li><strong>Paste </strong>
-					<ul>
-						<li><strong>To New Alignment (Control Shift V)<br>
-						</strong><em>A new alignment window will be created from sequences
-								previously copied or cut to the system clipboard. <br> Use
-								&lt;CTRL&gt; and &lt;SHIFT&gt; and V(&lt;APPLE&gt; and
-								&lt;SHIFT;&gt; and and V on MacOSX) to paste.</em>
-						</li>
-						<li><strong>Add To This Alignment (Control V)<br>
-						</strong><em>Copied sequences from another alignment window can be
-								added to the current Jalview alignment. </em>
-						</li>
-					</ul></li>
-				<li><strong>Delete (Backspace)<br> </strong><em>This
-						will delete the currently selected residues without copying them
-						to the clipboard. Like the other edit operations, this can be
-						undone with <strong>Undo</strong>.</em>
-				</li>
-				<li><strong>Remove Left (Control L)<br> </strong><em>If
-						the alignment has marked columns, the alignment will be trimmed to
-						the left of the leftmost marked column. To mark a column, mouse
-						click the scale bar above the alignment. Click again to unmark a
-						column, or select &quot;Deselect All&quot; to deselect all
-						columns.</em></li>
-				<li><strong>Remove Right (Control R)<br> </strong><em>If
-						the alignment has marked columns, the alignment will be trimmed to
-						the left of the leftmost marked column. To mark a column, mouse
-						click the scale bar above the alignment. Click again to unmark a
-						column, or select &quot;Deselect All&quot; to deselect all
-						columns.</em></li>
-				<li><strong>Remove Empty Columns (Control E)<br>
-				</strong><em>All columns which only contain gap characters
-						(&quot;-&quot;, &quot;.&quot;) will be deleted.<br> You may
-						set the default gap character in <a
-						href="../features/preferences.html">preferences</a>. </em>
-				</li>
-				<li><strong>Remove All Gaps (Control Shift E)</strong><br>
-					<em>Gap characters (&quot;-&quot;, &quot;.&quot;) will be
-						deleted from the selected area of the alignment. If no selection
-						is made, ALL the gaps in the alignment will be removed.<br>
-						You may set the default gap character in <a
-						href="../features/preferences.html">preferences</a>. </em>
-				</li>
-				<li><strong>Remove Redundancy (Control D)<br> </strong><em>Selecting
-						this option brings up a window asking you to select a threshold.
-						If the percentage identity between any two sequences (under the
-						current alignment) exceeds this value then one of the sequences
-						(the shorter) is discarded. Press the &quot;Apply&quot; button to
-						remove redundant sequences. The &quot;Undo&quot; button will undo
-						the last redundancy deletion.</em>
-				</li>
-				<li><strong>Pad Gaps<br> </strong><em>When selected,
-						the alignment will be kept at minimal width (so there are no empty
-						columns before or after the first or last aligned residue) and all
-						sequences will be padded with gap characters before and
-						after their terminating residues.<br> This switch is useful
-						when making a tree using unaligned sequences and when working with
-						alignment analysis programs which require 'properly aligned
-						sequences' to be all the same length.<br> You may set the
-						default for <strong>Pad Gaps</strong> in the <a
-						href="../features/preferences.html">preferences</a>. </em>
-				</li>
-			</ul></li>
-		<li><strong>Select</strong>
-			<ul>
-  <li><a href="../features/search.html"><strong>Find... (Control F)</strong></a><br>
-    <em>Opens the Find dialog box to search for residues, sequence name or residue 
-    position within the alignment and create new sequence features from the queries. 
-    </em>
-  <li><strong>Select All (Control A)</strong><strong><br>
-    </strong><em>Selects all the sequences and residues in the alignment. <br>
-    Use &lt;CTRL&gt; and A (&lt;APPLE&gt; and A on a MacOSX) to select all.</em></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 marked columns
-	will be deselected. </em><em> <br>
-	Use &lt;ESCAPE&gt; to deselect all.</em></li>
-	<li><strong>Invert Sequence Selection (Control I)<br>
-	</strong><em>Any sequence ids currently not selected will replace the
-	current selection. </em></li>
-	<li><strong>Invert Column Selection (Control Alt I)<br>
-	</strong><em>Any columns currently not selected will replace the current
-	column selection. </em></li>
-	<li><strong>Create Group (Control G)<br></strong>
-	<em>Create a group containing the currently selected sequences.</em></li>
-  <li><strong>Remove Group (Shift Control G)<br></strong>
-  <em>Ungroup the currently selected sequence group.</em></li>
-		<li><strong>Make Groups for selection<br /></strong> <em>The
-				currently selected groups of the alignment will be subdivided
-				according to the contents of the currently selected region. <br />Use
-				this to subdivide an alignment based on the different combinations
-				of residues at marked columns.
-		</em></li>
-		<li><strong>Undefine Groups (Control U)<br>
-  </strong><em>The alignment will be reset with no defined groups.<br>
-  <strong>WARNING</strong>: This cannot be undone.</em></li>
-    <li><strong><a
-        href="../features/columnFilterByAnnotation.html">Select/Hide Columns by Annotation</a></strong> <br />
-      <em>Select or Hide columns in the alignment according to
-        secondary structure, labels and values shown in alignment
-        annotation rows. </em></li>
-  		</ul></li>
-		<li><strong>View</strong>
-			<ul>
-				<li><strong>New View (Control T)</strong><em><br>
-						Creates a new view from the current alignment view. </em>
-				</li>
-				<li><strong>Expand Views (X)</strong><em><br> Display
-						each view associated with the alignment in its own alignment
-						window, allowing several views to be displayed simultaneously. </em>
-				</li>
-				<li><strong>Gather Views (G)</strong><em><br> Each
-						view associated with the alignment will be displayed within its
-						own tab on the current alignment window. </em>
-				</li>
-				<li><strong>Show&#8594;(all Columns / Sequences /
-						Sequences and Columns)</strong><em><br> All hidden Columns /
-						Sequences / Sequences and Columns will be revealed. </em>
-				</li>
-				<li><strong>Hide&#8594;(all Columns / Sequences /
-						Selected Region / All but Selected Region )</strong><em><br>
-						Hides the all the currently selected Columns / Sequences / Region
-						or everything but the selected Region.</em>
-				</li>
-				<li><strong>Automatic Scrolling<br> </strong><em>When
-						selected, the view will automatically scroll to display the
-						highlighted sequence position corresponding to the position under
-						the mouse pointer in a linked alignment or structure view.</em></li>
-				<li><strong>Show Sequence Features</strong><br> <em>Show
-						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
-							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 servers.</em>
-				</li>
-				<li><strong>Sequence ID Tooltip</strong><em> (application
-						only) <br>This submenu's options allow the inclusion or
-						exclusion of non-positional sequence features or database cross
-						references from the tooltip shown when the mouse hovers over the
-						sequence ID panel.</em>
-				</li>
-				<li><strong>Alignment Properties...<br /> </strong><em>Displays
-						some simple statistics computed for the current alignment view and
-						any named properties defined on the whole alignment.</em>
-				</li>
-				<li><strong><a href="../features/overview.html">Overview
-							Window</a><br> </strong><em>A scaled version of the alignment will
-						be displayed in a small window. A red box will indicate the
-						currently visible area of the alignment. Move the visible region
-						using the mouse. </em>
-				</li>
-			</ul></li>
-		<li><strong>Annotations</strong><em> (Since Jalview 2.8.2)</em>
-			<ul>
-			  <li><strong>Show Annotations<br> </strong><em>If this
-						is selected the &quot;Annotation Panel&quot; will be displayed
-						below the alignment. The default setting is to display the
-						conservation calculation, quality calculation and consensus values
-						as bar charts. </em>
-			  </li>
-			  <li><strong>Show Alignment Related</strong><em><br>
-			    Show all annotations that are for the alignment as a whole (for example, Consensus, 
-			    or secondary structure prediction from alignment).</em></li>
-			  <li><strong>Hide Alignment Related</strong><em><br>
-			    Hide all annotations that are for the alignment as a whole.</em></li>
-			  <li><strong>Show Sequence Related</strong><em><br>
-			    Show all annotations that are for individual sequences.</em></li>
-			  <li><strong>Hide Sequence Related</strong><em><br>
-			    Hide all annotations that are for individual sequences.</em></li>
-			  <li><em>You can also selectively show or hide annotations from the <a href="./popupMenu.html">Popup</a> 
-			    or <a href="../features/annotation.html">Annotation</a> menus.</em></li>
-			  <li><strong>Sort by Sequence</strong><em><br>Sort sequence-specific annotations by sequence order in the alignment
-			  (and within that, by label).</em></li>
-			  <li><strong>Sort by Label</strong><em><br>Sort sequence-specific annotations by label
-			  (and within that, by sequence order). If neither sort order is selected, no sorting is applied,
-			  allowing you to make a manual ordering of the annotations.</em></li>
-			  <li><strong>Autocalculated Annotation<br> </strong><em>Settings
-					for the display of autocalculated annotation.</em>
-					<ul>
-					    <li><strong>Show first<br></strong><em>
-					      Show autocalculated annotations above sequence-specific annotations.
-					      Note this also applies to other annotations for the alignment, for example secondary
-					      structure prediction from alignment.</em></li>
-					    <li><strong>Show last<br></strong><em>
-					      Show autocalculated / alignment annotations below sequence-specific annotations.</em></li>
-						<li><strong>Apply to all groups<br> </strong><em> When
-							ticked, any modification to the current settings will be applied
-							to all autocalculated annotation.</em></li>
-						<li><strong>Show Consensus Histogram<br> </strong><em>
-							Enable or disable the display of the histogram above the
-							consensus sequence.</em></li>
-						<li><strong>Show Consensus Logo<br> </strong><em> Enable
-							or disable the display of the Consensus Logo above the consensus
-							sequence.</em></li>
-						<li><strong>Normalise Consensus Logo<br>
-						</strong><em>When enabled, scales all logo stacks to the same height,
-								making it easier to compare symbol diversity in highly variable
-								regions.</em></li>
-						<li><strong>Group Conservation<br> </strong><em> When
-							ticked, display a conservation row for all groups (only available
-							for protein alignments).</em></li>
-						<li><strong>Group Consensus<br> </strong><em> When
-							ticked, display a consensus row for all groups.</em></li>
-					</ul>
-				</li>
-			</ul>
-		</li>
-		<li><strong>Alignment Window Format Menu</strong>
-			<ul>
-				<li><strong>Font...<br> </strong><em>Opens the
-						&quot;Choose Font&quot; dialog box, in order to change the font of
-						the display and enable or disable 'smooth fonts' (anti-aliasing)
-						for faster alignment rendering. </em></li>
-				<li><strong>Wrap<br> </strong><em>When ticked, the
-						alignment display is &quot;<a href="../features/wrap.html">wrapped</a>&quot;
-						to the width of the alignment window. This is useful if your
-						alignment has only a few sequences to view its full width at once.</em><br>
-					Additional options for display of sequence numbering and scales are
-					also visible in wrapped layout mode:<br>
-					<ul>
-						<li><strong>Scale Above</strong><br><em> Show the alignment
-							column position scale.</em></li>
-						<li><strong>Scale Left</strong><br><em> Show the sequence
-							position for the first aligned residue in each row in the left
-							column of the alignment.</em></li>
-						<li><strong>Scale Right</strong><br><em> Show the sequence
-							position for the last aligned residue in each row in the
-							right-most column of the alignment.</em></li>
-						<li><strong>Show Sequence Limits<br> </strong><em>If
-								this box is selected the sequence name will have the start and
-								end position of the sequence appended to the name, in the format
-								NAME/START-END</em>
-						</li>
-						<li><strong>Right Align Sequence ID<br> </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. 
-						</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>
-						<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 conjunction with
-								&quot;Colour Text.&quot; </em>
-						</li>
-						<li><strong>Text<br> </strong><em>If this is
-								selected the residues will be displayed using the standard 1
-								character amino acid alphabet.</em>
-						</li>
-						<li><strong>Colour Text<br> </strong><em>If this is
-								selected the residues will be coloured according to the
-								background colour associated with that residue. The colour is
-								slightly darker than background so the amino acid symbol remains
-								visible. </em>
-						</li>
-						<li><strong>Show Gaps<br> </strong><em>When this is
-								selected, gap characters will be displayed as &quot;.&quot; or
-								&quot;-&quot;. If unselected, then gap characters will appear as
-								blank spaces. <br> You may set the default gap character in
-								<a href="../features/preferences.html">preferences</a>.</em>
-						</li>
-						<li><strong>Centre Annotation Labels<br> </strong><em>Select
-								this to center labels along an annotation row relative to their
-								associated column (default is off, i.e. left-justified).</em>
-						</li>
-						<li><strong>Show Unconserved<br> </strong><em>When
-								this is selected, all consensus sequence symbols will be
-								rendered as a '.', highlighting mutations in highly conserved
-								alignments. </em>
-						</li>
+            features visible on the alignment can be saved to file or
+            displayed in a textbox in either Jalview or GFF format</em></li>
+        <li><strong>Export Annotations</strong><em><br>
+            All annotations visible on the alignment can be saved to
+            file or displayed in a textbox in Jalview annotations
+            format. </em></li>
+        <li><strong>Load Associated Tree<br>
+        </strong><em>Jalview can <a href="../calculations/treeviewer.html">view
+              trees</a> stored in the Newick file format, and associate them
+            with the alignment. Note: the ids of the tree file and your
+            alignment MUST be the same.
+        </em></li>
+        <li><strong>Load Features / Annotations<br>
+        </strong><em>Load files describing precalculated <a
+            href="../features/featuresFormat.html"
+          >sequence features</a> or <a
+            href="../features/annotationsFormat.html"
+          >alignment annotations</a>.
+        </em></li>
+        <li><strong>Close (Control W)</strong><br> <em>Close
+            the alignment window. Make sure you have saved your
+            alignment before you close - either from the Desktop's <strong>Save
+              Project</strong> File menu option, or by using the <strong>Save
+              As</strong> menu.
+        </em></li>
+      </ul></li>
+    <li><strong>Edit</strong>
+      <ul>
+        <li><strong>Undo (Control Z)</strong><em><br>
+            This will undo any edits you make to the alignment. This
+            applies to insertion or deletion of gaps, cutting residues
+            or sequences from the alignment or pasting sequences to the
+            current alignment or sorting the alignment. <strong>NOTE:</strong>
+            It DOES NOT undo colour changes, adjustments to group sizes,
+            or changes to the annotation panel. </em></li>
+        <li><strong>Redo (Control Y)<br>
+        </strong><em>Any actions which you undo can be redone using redo. </em></li>
+        <li><strong>Cut (Control X)<br>
+        </strong><em>This will make a copy of the currently selected
+            residues before removing them from your alignment. Click on
+            a sequence name if you wish to select a whole sequence. <br>
+            Use &lt;CTRL&gt; and X (&lt;APPLE&gt; and X on MacOSX) to
+            cut.
+        </em></li>
+        <li><strong>Copy (Control C)</strong><br> <em>Copies
+            the currently selected residues to the system clipboard -
+            you can also do this by pressing &lt;CTRL&gt; and C
+            (&lt;APPLE&gt; and C on MacOSX). <br> If you try to
+            paste the clipboard contents to a text editor, you will see
+            the format of the copied residues FASTA.
+        </em></li>
+        <li><strong>Paste </strong>
+          <ul>
+            <li><strong>To New Alignment (Control Shift V)<br>
+            </strong><em>A new alignment window will be created from
+                sequences previously copied or cut to the system
+                clipboard. <br> Use &lt;CTRL&gt; and &lt;SHIFT&gt;
+                and V(&lt;APPLE&gt; and &lt;SHIFT;&gt; and and V on
+                MacOSX) to paste.
+            </em></li>
+            <li><strong>Add To This Alignment (Control V)<br>
+            </strong><em>Copied sequences from another alignment window can
+                be added to the current Jalview alignment. </em></li>
+          </ul></li>
+        <li><strong>Delete (Backspace)<br>
+        </strong><em>This will delete the currently selected residues
+            without copying them to the clipboard. Like the other edit
+            operations, this can be undone with <strong>Undo</strong>.
+        </em></li>
+        <li><strong>Remove Left (Control L)<br>
+        </strong><em>If the alignment has marked columns, the alignment will
+            be trimmed to the left of the leftmost marked column. To
+            mark a column, mouse click the scale bar above the
+            alignment. Click again to unmark a column, or select
+            &quot;Deselect All&quot; to deselect all columns.</em></li>
+        <li><strong>Remove Right (Control R)<br>
+        </strong><em>If the alignment has marked columns, the alignment will
+            be trimmed to the left of the leftmost marked column. To
+            mark a column, mouse click the scale bar above the
+            alignment. Click again to unmark a column, or select
+            &quot;Deselect All&quot; to deselect all columns.</em></li>
+        <li><strong>Remove Empty Columns (Control E)<br>
+        </strong><em>All columns which only contain gap characters
+            (&quot;-&quot;, &quot;.&quot;) will be deleted.<br> You
+            may set the default gap character in <a
+            href="../features/preferences.html"
+          >preferences</a>.
+        </em></li>
+        <li><strong>Remove All Gaps (Control Shift E)</strong><br>
+          <em>Gap characters (&quot;-&quot;, &quot;.&quot;) will be
+            deleted from the selected area of the alignment. If no
+            selection is made, ALL the gaps in the alignment will be
+            removed.<br> You may set the default gap character in <a
+            href="../features/preferences.html"
+          >preferences</a>.
+        </em></li>
+        <li><strong>Remove Redundancy (Control D)<br>
+        </strong><em>Selecting this option brings up a window asking you to
+            select a threshold. If the percentage identity between any
+            two sequences (under the current alignment) exceeds this
+            value then one of the sequences (the shorter) is discarded.
+            Press the &quot;Apply&quot; button to remove redundant
+            sequences. The &quot;Undo&quot; button will undo the last
+            redundancy deletion.</em></li>
+        <li><strong>Pad Gaps<br>
+        </strong><em>When selected, the alignment will be kept at minimal
+            width (so there are no empty columns before or after the
+            first or last aligned residue) and all sequences will be
+            padded with gap characters before and after their
+            terminating residues.<br> This switch is useful when
+            making a tree using unaligned sequences and when working
+            with alignment analysis programs which require 'properly
+            aligned sequences' to be all the same length.<br> You
+            may set the default for <strong>Pad Gaps</strong> in the <a
+            href="../features/preferences.html"
+          >preferences</a>.
+        </em></li>
+      </ul></li>
+    <li><strong>Select</strong>
+      <ul>
+        <li><a href="../features/search.html"><strong>Find...
+              (Control F)</strong></a><br> <em>Opens the Find dialog box to
+            search for residues, sequence name or residue position
+            within the alignment and create new sequence features from
+            the queries. </em>
+        <li><strong>Select All (Control A)</strong><strong><br>
+        </strong><em>Selects all the sequences and residues in the
+            alignment. <br> Use &lt;CTRL&gt; and A (&lt;APPLE&gt;
+            and A on a MacOSX) to select all.
+        </em></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
+            marked columns will be deselected. </em><em> <br> Use
+            &lt;ESCAPE&gt; to deselect all.
+        </em></li>
+        <li><strong>Invert Sequence Selection (Control I)<br>
+        </strong><em>Any sequence ids currently not selected will replace
+            the current selection. </em></li>
+        <li><strong>Invert Column Selection (Control Alt
+            I)<br>
+        </strong><em>Any columns currently not selected will replace the
+            current column selection. </em></li>
+        <li><strong>Create Group (Control G)<br></strong> <em>Create
+            a group containing the currently selected sequences.</em></li>
+        <li><strong>Remove Group (Shift Control G)<br></strong>
+          <em>Ungroup the currently selected sequence group.</em></li>
+        <li><strong>Make Groups for selection<br /></strong> <em>The
+            currently selected groups of the alignment will be
+            subdivided according to the contents of the currently
+            selected region. <br />Use this to subdivide an alignment
+            based on the different combinations of residues at marked
+            columns.
+        </em></li>
+        <li><strong>Undefine Groups (Control U)<br>
+        </strong><em>The alignment will be reset with no defined groups.<br>
+            <strong>WARNING</strong>: This cannot be undone.
+        </em></li>
+        <li><strong><a
+            href="../features/columnFilterByAnnotation.html"
+          >Select/Hide Columns by Annotation</a></strong> <br /> <em>Select
+            or Hide columns in the alignment according to secondary
+            structure, labels and values shown in alignment annotation
+            rows. </em></li>
+      </ul></li>
+    <li><strong>View</strong>
+      <ul>
+        <li><strong>New View (Control T)</strong><em><br>
+            Creates a new view from the current alignment view. </em></li>
+        <li><strong>Expand Views (X)</strong><em><br>
+            Display each view associated with the alignment in its own
+            alignment window, allowing several views to be displayed
+            simultaneously. </em></li>
+        <li><strong>Gather Views (G)</strong><em><br>
+            Each view associated with the alignment will be displayed
+            within its own tab on the current alignment window. </em></li>
+        <li><strong>Show&#8594;(all Columns / Sequences /
+            Sequences and Columns)</strong><em><br> All hidden Columns
+            / Sequences / Sequences and Columns will be revealed. </em></li>
+        <li><strong>Hide&#8594;(all Columns / Sequences /
+            Selected Region / All but Selected Region )</strong><em><br>
+            Hides the all the currently selected Columns / Sequences /
+            Region or everything but the selected Region.</em></li>
+        <li><strong>Automatic Scrolling<br>
+        </strong><em>When selected, the view will automatically scroll to
+            display the highlighted sequence position corresponding to
+            the position under the mouse pointer in a linked alignment
+            or structure view.</em></li>
+        <li><strong>Show Sequence Features</strong><br> <em>Show
+            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 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
+              servers.</em></li>
+        <li><strong>Sequence ID Tooltip</strong><em>
+            (application only) <br>This submenu's options allow the
+            inclusion or exclusion of non-positional sequence features
+            or database cross references from the tooltip shown when the
+            mouse hovers over the sequence ID panel.
+        </em></li>
+        <li><strong>Alignment Properties...<br />
+        </strong><em>Displays some simple statistics computed for the
+            current alignment view and any named properties defined on
+            the whole alignment.</em></li>
+        <li><strong><a href="../features/overview.html">Overview
+              Window</a><br> </strong><em>A scaled version of the alignment
+            will be displayed in a small window. A red box will indicate
+            the currently visible area of the alignment. Move the
+            visible region using the mouse. </em></li>
+      </ul></li>
+    <li><strong>Annotations</strong><em> (Since Jalview 2.8.2)</em>
+      <ul>
+        <li><strong>Show Annotations<br>
+        </strong><em>If this is selected the &quot;Annotation Panel&quot;
+            will be displayed below the alignment. The default setting
+            is to display the conservation calculation, quality
+            calculation and consensus values as bar charts. </em></li>
+        <li><strong>Show Alignment Related</strong><em><br>
+            Show all annotations that are for the alignment as a whole
+            (for example, Consensus, or secondary structure prediction
+            from alignment).</em></li>
+        <li><strong>Hide Alignment Related</strong><em><br>
+            Hide all annotations that are for the alignment as a whole.</em></li>
+        <li><strong>Show Sequence Related</strong><em><br>
+            Show all annotations that are for individual sequences.</em></li>
+        <li><strong>Hide Sequence Related</strong><em><br>
+            Hide all annotations that are for individual sequences.</em></li>
+        <li><em>You can also selectively show or hide
+            annotations from the <a href="./popupMenu.html">Popup</a> or
+            <a href="../features/annotation.html">Annotation</a> menus.
+        </em></li>
+        <li><strong>Sort by Sequence</strong><em><br>Sort
+            sequence-specific annotations by sequence order in the
+            alignment (and within that, by label).</em></li>
+        <li><strong>Sort by Label</strong><em><br>Sort
+            sequence-specific annotations by label (and within that, by
+            sequence order). If neither sort order is selected, no
+            sorting is applied, allowing you to make a manual ordering
+            of the annotations.</em></li>
+        <li><strong>Autocalculated Annotation<br>
+        </strong><em>Settings for the display of autocalculated annotation.</em>
+          <ul>
+            <li><strong>Show first<br></strong><em> Show
+                autocalculated annotations above sequence-specific
+                annotations. Note this also applies to other annotations
+                for the alignment, for example secondary structure
+                prediction from alignment.</em></li>
+            <li><strong>Show last<br></strong><em> Show
+                autocalculated / alignment annotations below
+                sequence-specific annotations.</em></li>
+            <li><strong>Apply to all groups<br>
+            </strong><em> When ticked, any modification to the current
+                settings will be applied to all autocalculated
+                annotation.</em></li>
+            <li><strong>Show Consensus Histogram<br>
+            </strong><em> Enable or disable the display of the histogram
+                above the consensus sequence.</em></li>
+            <li><strong>Show Consensus Logo<br>
+            </strong><em> Enable or disable the display of the Consensus
+                Logo above the consensus sequence.</em></li>
+            <li><strong>Normalise Consensus Logo<br>
+            </strong><em>When enabled, scales all logo stacks to the same
+                height, making it easier to compare symbol diversity in
+                highly variable regions.</em></li>
+            <li><strong>Group Conservation<br>
+            </strong><em> When ticked, display a conservation row for all
+                groups (only available for protein alignments).</em></li>
+            <li><strong>Group Consensus<br>
+            </strong><em> When ticked, display a consensus row for all
+                groups.</em></li>
+          </ul></li>
+      </ul></li>
+    <li><strong>Alignment Window Format Menu</strong>
+      <ul>
+        <li><strong>Font...<br>
+        </strong><em>Opens the &quot;Choose Font&quot; dialog box, in order
+            to change the font of the display and enable or disable
+            'smooth fonts' (anti-aliasing) for faster alignment
+            rendering. </em></li>
+        <li><strong>Wrap<br>
+        </strong><em>When ticked, the alignment display is &quot;<a
+            href="../features/wrap.html"
+          >wrapped</a>&quot; to the width of the alignment window. This is
+            useful if your alignment has only a few sequences to view
+            its full width at once.
+        </em><br> Additional options for display of sequence numbering
+          and scales are also visible in wrapped layout mode:<br>
+          <ul>
+            <li><strong>Scale Above</strong><br>
+            <em> Show the alignment column position scale.</em></li>
+            <li><strong>Scale Left</strong><br>
+            <em> Show the sequence position for the first aligned
+                residue in each row in the left column of the alignment.</em></li>
+            <li><strong>Scale Right</strong><br>
+            <em> Show the sequence position for the last aligned
+                residue in each row in the right-most column of the
+                alignment.</em></li>
+            <li><strong>Show Sequence Limits<br>
+            </strong><em>If this box is selected the sequence name will have
+                the start and end position of the sequence appended to
+                the name, in the format NAME/START-END</em></li>
+            <li><strong>Right Align Sequence ID<br>
+            </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.
+            </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>
+            <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
+                conjunction with &quot;Colour Text.&quot; </em></li>
+            <li><strong>Text<br>
+            </strong><em>If this is selected the residues will be displayed
+                using the standard 1 character amino acid alphabet.</em></li>
+            <li><strong>Colour Text<br>
+            </strong><em>If this is selected the residues will be coloured
+                according to the background colour associated with that
+                residue. The colour is slightly darker than background
+                so the amino acid symbol remains visible. </em></li>
+            <li><strong>Show Gaps<br>
+            </strong><em>When this is selected, gap characters will be
+                displayed as &quot;.&quot; or &quot;-&quot;. If
+                unselected, then gap characters will appear as blank
+                spaces. <br> You may set the default gap character
+                in <a href="../features/preferences.html">preferences</a>.
+            </em></li>
+            <li><strong>Centre Annotation Labels<br>
+            </strong><em>Select this to center labels along an annotation
+                row relative to their associated column (default is off,
+                i.e. left-justified).</em></li>
+            <li><strong>Show Unconserved<br>
+            </strong><em>When this is selected, all consensus sequence
+                symbols will be rendered as a '.', highlighting
+                mutations in highly conserved alignments. </em></li>
 
-					</ul></li>
-			</ul>
-	</li>
+          </ul></li>
+      </ul></li>
 
-		</ul>
-		</li>
+  </ul>
+  </li>
 
-		<li><strong>Colour</strong>
-			<ul>
-				<li><strong>Apply Colour To All Groups<br> </strong><em>If
-						this is selected, any changes made to the background colour will
-						be applied to all currently defined groups.<br> </em>
-				</li>
-				<li><strong><a href="../colourSchemes/textcolour.html">Colour
-							Text...</a> </strong><em><br> Opens the Colour Text dialog box to
-						set a different text colour for light and dark background, and the
-						intensity threshold for transition between them. </em>
-				</li>
-				<li>Colour Scheme options: <strong>None, ClustalX,
-						Blosum62 Score, Percentage Identity, Zappo, Taylor,
-						Hydrophobicity, Helix Propensity, Strand Propensity, Turn
-						Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User Defined<br> </strong> <em>See
-						<a href="../colourSchemes/index.html">colours</a> for a
-						description of all colour schemes.</em><br></li>
-				<li><strong>By Conservation<br> </strong><em>See <a
-						href="../colourSchemes/conservation.html">Colouring by
-							Conservation</a>.</em><br></li>
-				<li><strong>Modify Conservation Threshold<br> </strong><em>Use
-						this to display the conservation threshold slider window. Useful
-						if the window has been closed, or if the 'by conservation' option
-						appears to be doing nothing!</em><br></li>
-				<li><strong>Above Identity Threshold<br> </strong><em>See
-						<a href="../colourSchemes/abovePID.html">Above Percentage
-							Identity</a> </em><strong>.<br> </strong>
-				</li>
-				<li><strong>Modify Identity Threshold<br> </strong><em>Use
-						this to set the threshold value for colouring above Identity.
-						Useful if the window has been closed.<br> </em>
-				</li>
-				<li><strong>By Annotation</strong><br> <em>Colours
-						the alignment on a per-column value from a specified annotation.
-						See <a href="../colourSchemes/annotationColouring.html">Annotation
-							Colouring</a>.</em><br></li>
-		<li><strong>By RNA Helices</strong><br>
-		<em>Colours the helices of an RNA alignment loaded from a Stockholm file. See 
-		<a href="../colourSchemes/rnahelicesColouring.html">RNA Helices
-		Colouring</a>.</em><br>
-		</li>
-			</ul></li>
-		<li><strong>Calculate</strong>
-			<ul>
-				<li><strong>Sort </strong>
-					<ul>
-						<li><strong>by ID</strong><em><br> This will sort
-								the sequences according to sequence name. If the sort is
-								repeated, the order of the sorted sequences will be inverted. </em>
-						</li>
-						<li><strong>by Length</strong><em><br> This will
-								sort the sequences according to their length (excluding gap
-								characters). If the sort is repeated, the order of the sorted
-								sequences will be inverted. </em></li>
-						<li><strong>by Group</strong><strong><br> </strong><em>This
-								will sort the sequences according to sequence name. If the sort
-								is repeated, the order of the sorted sequences will be inverted.
-						</em><strong></strong></li>
-						<li><strong>by Pairwise Identity<br> </strong><em>This
-								will sort the selected sequences by their percentage identity to
-								the consensus sequence. The most similar sequence is put at the
-								top. </em></li>
-						<li><em>The <a href="../calculations/sorting.html">Sort
-									menu</a> will have some additional options if you have just done a
-								multiple alignment calculation, or opened a tree viewer window.</em><br>
-						</li>
-					</ul>
-				</li>
+  <li><strong>Colour</strong>
+    <ul>
+      <li><strong>Apply Colour To All Groups<br>
+      </strong><em>If this is selected, any changes made to the background
+          colour will be applied to all currently defined groups.<br>
+      </em></li>
+      <li><strong><a
+          href="../colourSchemes/textcolour.html"
+        >Colour Text...</a> </strong><em><br> Opens the Colour Text
+          dialog box to set a different text colour for light and dark
+          background, and the intensity threshold for transition between
+          them. </em></li>
+      <li>Colour Scheme options: <strong>None, ClustalX,
+          Blosum62 Score, Percentage Identity, Zappo, Taylor,
+          Hydrophobicity, Helix Propensity, Strand Propensity, Turn
+          Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User
+          Defined<br>
+      </strong> <em>See <a href="../colourSchemes/index.html">colours</a>
+          for a description of all colour schemes.
+      </em><br></li>
+      <li><strong>By Conservation<br>
+      </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
+            by Conservation</a>.
+      </em><br></li>
+      <li><strong>Modify Conservation Threshold<br>
+      </strong><em>Use this to display the conservation threshold slider
+          window. Useful if the window has been closed, or if the 'by
+          conservation' option appears to be doing nothing!</em><br></li>
+      <li><strong>Above Identity Threshold<br>
+      </strong><em>See <a href="../colourSchemes/abovePID.html">Above
+            Percentage Identity</a>
+      </em><strong>.<br>
+      </strong></li>
+      <li><strong>Modify Identity Threshold<br>
+      </strong><em>Use this to set the threshold value for colouring above
+          Identity. Useful if the window has been closed.<br>
+      </em></li>
+      <li><strong>By Annotation</strong><br> <em>Colours
+          the alignment on a per-column value from a specified
+          annotation. See <a
+          href="../colourSchemes/annotationColouring.html"
+        >Annotation Colouring</a>.
+      </em><br></li>
+      <li><strong>By RNA Helices</strong><br> <em>Colours
+          the helices of an RNA alignment loaded from a Stockholm file.
+          See <a href="../colourSchemes/rnahelicesColouring.html">RNA
+            Helices Colouring</a>.
+      </em><br></li>
+    </ul></li>
+  <li><strong>Calculate</strong>
+    <ul>
+      <li><strong>Sort </strong>
+        <ul>
+          <li><strong>by ID</strong><em><br> This will
+              sort the sequences according to sequence name. If the sort
+              is repeated, the order of the sorted sequences will be
+              inverted. </em></li>
+          <li><strong>by Length</strong><em><br> This
+              will sort the sequences according to their length
+              (excluding gap characters). If the sort is repeated, the
+              order of the sorted sequences will be inverted. </em></li>
+          <li><strong>by Group</strong><strong><br> </strong><em>This
+              will sort the sequences according to sequence name. If the
+              sort is repeated, the order of the sorted sequences will
+              be inverted. </em><strong></strong></li>
+          <li><strong>by Pairwise Identity<br>
+          </strong><em>This will sort the selected sequences by their
+              percentage identity to the consensus sequence. The most
+              similar sequence is put at the top. </em></li>
+          <li><em>The <a href="../calculations/sorting.html">Sort
+                menu</a> will have some additional options if you have just
+              done a multiple alignment calculation, or opened a tree
+              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
@@ -525,108 +561,118 @@
         </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>.</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&#8594;Score menu.</em> <br>
-				</li>
-				<li><strong>Autocalculate Consensus</strong><br> <em>For
-						large alignments it can be useful to deselect &quot;Autocalculate
-						Consensus&quot; when editing. This prevents the sometimes lengthy
-						calculations performed after each sequence edit.</em> <br>
-				</li>
-				<li><strong>Sort With New Tree</strong><br> <em>When
-						enabled, Jalview will automatically sort the alignment when a new
-						tree is calculated or loaded onto it.</em> <br></li>
-			<li><strong>Show Flanking Regions</strong><br> <em>Opens
-					a new alignment window showing any additional sequence data either
-					side of the current alignment. Useful in conjunction with 'Fetch
-					Database References' when the 'Trim Retrieved Sequences' option is
-					disabled to retrieve full length sequences for a set of aligned
-					peptides. </em></li>
-		</ul></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 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&#8594;Score menu.
+      </em> <br></li>
+      <li><strong>Autocalculate Consensus</strong><br> <em>For
+          large alignments it can be useful to deselect
+          &quot;Autocalculate Consensus&quot; when editing. This
+          prevents the sometimes lengthy calculations performed after
+          each sequence edit.</em> <br></li>
+      <li><strong>Sort With New Tree</strong><br> <em>When
+          enabled, Jalview will automatically sort the alignment when a
+          new tree is calculated or loaded onto it.</em> <br></li>
+      <li><strong>Show Flanking Regions</strong><br> <em>Opens
+          a new alignment window showing any additional sequence data
+          either side of the current alignment. Useful in conjunction
+          with 'Fetch Database References' when the 'Trim Retrieved
+          Sequences' option is disabled to retrieve full length
+          sequences for a set of aligned peptides. </em></li>
+    </ul></li>
 
-		<li><strong>Web Service Menu</strong><br /> <em>This menu
-				is dynamic, and may contain user-defined web service entries in
-				addition to any of the following ones:</em>
-			<ul>
-				<li><strong>Fetch DB References</strong><br> <em>This
-        submenu contains options for accessing any of the database services
-        that Jalview is aware of (e.g. DAS sequence servers and the
-        WSDBFetch service provided by the EBI) to verify sequence start/end
-        positions and retrieve all database cross references and PDB ids
-        associated with all or just the selected sequences in the alignment.
+  <li><strong>Web Service Menu</strong><br /> <em>This menu
+      is dynamic, and may contain user-defined web service entries in
+      addition to any of the following ones:</em>
+    <ul>
+      <li><strong>Fetch DB References</strong><br> <em>This
+          submenu contains options for accessing any of the database
+          services that Jalview is aware of (e.g. DAS sequence servers
+          and the WSDBFetch service provided by the EBI) to verify
+          sequence start/end positions and retrieve all database cross
+          references and PDB ids associated with all or just the
+          selected sequences in the alignment.
+          <ul>
+            <li>'Trim Retrieved Sequences' - when checked, Jalview
+              will discard any additional sequence data for accessions
+              associated with sequences in the alignment. <br> <strong>Note:
+                Disabling this could cause out of memory errors when
+                working with genomic sequence records !</strong><br> <strong>Added
+                in Jalview 2.8.1</strong>
+            </li>
+            <li>'Standard Databases' will check sequences against
+              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.
+      </em><br></li>
+    </ul>
+    <p>Selecting items from the following submenus will start a
+      remote service on compute facilities at the University of Dundee,
+      or elsewhere. You need a continuous network connection in order to
+      use these services through Jalview.</p>
+    <ul>
+      <li><strong>Alignment</strong><br />
+      <em> Align the currently selected sequences or all sequences
+          in the alignment, or re-align unaligned sequences to the
+          aligned sequences. Entries in this menu provide access to the
+          various alignment programs supported by <a
+          href="../webServices/JABAWS.html"
+        >JABAWS</a>. See the <a href="../webServices/msaclient.html">Multiple
+            Sequence Alignment webservice client</a> entry for more
+          information.
+      </em></li>
+      <li><strong>Secondary Structure Prediction</strong>
+        <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>
+              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
+                  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
+                  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>
+                  sequence in the set (that is, the one that appears
+                  first in the alignment window).
+                </li>
+              </ul>
+          </em>
+        </ul></li>
+      <li><strong>Analysis</strong><br />
         <ul>
-          <li>'Trim Retrieved Sequences' - when checked, Jalview will
-            discard any additional sequence data for accessions associated with
-            sequences in the alignment. <br> <strong>Note: Disabling this
-              could cause out of memory errors when working with genomic
-              sequence records !</strong><br> <strong>Added in Jalview 2.8.1</strong>
-        </li>
-          <li>'Standard Databases' will check sequences against 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.
-    </em><br></li>
-			</ul>
-			<p>Selecting items from the following submenus will start a
-				remote service on compute facilities at the University of Dundee, or
-				elsewhere. You need a continuous network connection in order to use
-				these services through Jalview.
-			</p>
-			<ul>
-				<li><strong>Alignment</strong><br /><em> Align the currently
-					selected sequences or all sequences in the alignment, or re-align
-					unaligned sequences to the aligned sequences. Entries in this menu
-					provide access to the various alignment programs supported by <a
-					href="../webServices/JABAWS.html">JABAWS</a>. See the <a
-					href="../webServices/msaclient.html">Multiple Sequence
-						Alignment webservice client</a> entry for more information.</em></li>
-				<li><strong>Secondary Structure Prediction</strong>
-					<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> 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 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 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> sequence in the set
-										(that is, the one that appears first in the alignment window).
-									</li>
-								</ul> </em>
-					</ul></li>
-				<li><strong>Analysis</strong><br />
-					<ul>
-						<li><strong>Multi-Harmony</strong><br> <em>Performs
-								functional residue analysis on a protein family alignment with
-								sub-families defined on it. See the <a
-								href="../webServices/shmr.html">Multi-Harmony service</a> entry for more
-								information.</em>
-						</li>
-					</ul></li>
-			</ul></li>
-	</ul>
+          <li><strong>Multi-Harmony</strong><br> <em>Performs
+              functional residue analysis on a protein family alignment
+              with sub-families defined on it. See the <a
+              href="../webServices/shmr.html"
+            >Multi-Harmony service</a> entry for more information.
+          </em></li>
+        </ul></li>
+    </ul></li>
+  </ul>
 
 </body>
 </html>
