- <li><strong>Fetch Sequence</strong><br>
- <em>Shows a dialog window in which you can select known ids from
- Uniprot, EMBL, EMBLCDS 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 &
- 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 "Files of type:" 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 "Copy and Paste" using the pull down
- menu, or your standard operating system copy and paste keys. The
- output window also has a <strong>"New Window"</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> <em></em></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>
- </ul>
- </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>
- </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 &
+ 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 "Files of type:" 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 "Copy and Paste" using the pull down menu, or
+ your standard operating system copy and paste keys. The output
+ window also has a <strong>"New Window"</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>
+ </ul></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>
+ </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 as a Jalview project 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><strong><a href="../features/search.html">Find...
+ (Control F)</a> </strong><em><br> 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>
+ <li><strong>Select All (Control A)<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></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. (Create/Remove group new in Jalview 2.8.1)</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 observed at specific positions. (new in jalview 2.5)</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>
+ </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>