- 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 <CTRL> and X
- (<APPLE> 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 <CTRL> and C (<APPLE> 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
- <CTRL> and <SHIFT> and V(<APPLE> and
- <SHIFT;> 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 "Deselect All" 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 "Deselect All" to deselect all
- columns.</em></li>
- <li><strong>Remove Empty Columns (Control E)<br>
- </strong><em>All columns which only contain gap characters
- ("-", ".") 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 ("-", ".") 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 "Apply" button to
- remove redundant sequences. The "Undo" 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 <CTRL> and A (<APPLE> 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 <ESCAPE> 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→(all Columns / Sequences /
- Sequences and Columns)</strong><em><br> All hidden Columns /
- Sequences / Sequences and Columns will be revealed. </em>
- </li>
- <li><strong>Hide→(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 "Annotation Panel" 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
- "Choose Font" 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 "<a href="../features/wrap.html">wrapped</a>"
- 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
- "Colour Text." </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 "." or
- "-". 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 <CTRL> and X (<APPLE> 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 <CTRL> and C
+ (<APPLE> 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 <CTRL> and <SHIFT>
+ and V(<APPLE> and <SHIFT;> 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
+ "Deselect All" 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
+ "Deselect All" to deselect all columns.</em></li>
+ <li><strong>Remove Empty Columns (Control E)<br>
+ </strong><em>All columns which only contain gap characters
+ ("-", ".") 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 ("-", ".") 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 "Apply" button to remove redundant
+ sequences. The "Undo" 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 <CTRL> and A (<APPLE>
+ 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
+ <ESCAPE> 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→(all Columns / Sequences /
+ Sequences and Columns)</strong><em><br> All hidden Columns
+ / Sequences / Sequences and Columns will be revealed. </em></li>
+ <li><strong>Hide→(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 "Annotation Panel"
+ 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 "Choose Font" 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 "<a
+ href="../features/wrap.html"
+ >wrapped</a>" 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 "Colour Text." </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 "." or "-". 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>