-<html>
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
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- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
--->
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+ <title>Alignment Window Menus</title>
+
+
+</head><body>
+<p> <strong>Alignment Window Menus x</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 &
+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>
+ <script src="../scripts/supported_format.js"></script>
+ <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>
+ <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 no empty columns before or after the first or
+last aligned residue) and all sequences will be padded with gap
+characters to the 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 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>Autocalculated Annotation<br>
+ </strong><em>Settings for the display of autocalculated
+annotation.</em>
+ <ul>
+ <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>Apply to all groups<br>
+ </strong><em> When ticked, display a consensus row for all
+groups.</em></li>
+ </ul>
+ </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">Seqence
+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> </em></li>
+ <em> </em>
+ <li><em><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> </em></li>
+ <em> </em>
+ <li><em><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> </em></li>
+ <em> </em>
+ <li><em><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> </em></li>
+ <em> </em>
+ </ul>
+ </li>
+ <em> </em>
+ <li><em><strong>Alignment Window Format Menu</strong> </em>
+ <ul>
+ <em> </em>
+ <li><em><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></em></li>
+ <em> </em>
+ <li><em><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>
+ </em>
+ <ul>
+ <em> </em>
+ <li><em><strong>Scale Above</strong><br>
+ <em> Show the alignment column position scale.</em></em></li>
+ <em> </em>
+ <li><em><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></em></li>
+ <em> </em>
+ <li><em><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></em></li>
+ <em> </em>
+ <li><em><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> </em></li>
+ <em> </em>
+ <li><em><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. </em></em></li>
+ <em><em> </em></em>
+ <li><em><em><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. </em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><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> </em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><strong>Text<br>
+ </strong><em>If this is selected the residues will be
+displayed using the standard 1 character amino acid alphabet.</em> </em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><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> </em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><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> </em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><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> </em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><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> </em></em></em></li>
+ <em><em><em> </em></em></em>
+ </ul>
+ </li>
+ <em><em><em> </em></em></em>
+ </ul>
+ <em><em><em> </em></em></em></li>
+ <em><em><em> </em></em></em>
+</ul>
+
+<em><em><em> </em></em></em>
+<li><em><em><em><strong>Colour</strong> </em></em></em>
+ <ul>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><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> </em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><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> </em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em>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>
+ </em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><strong>By Conservation<br>
+ </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
+by Conservation</a>.</em><br>
+ </em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><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>
+ </em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><strong>Above Identity Threshold<br>
+ </strong><em>See <a href="../colourSchemes/abovePID.html">Above
+Percentage Identity</a> </em><strong>.<br>
+ </strong> </em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><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> </em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><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>
+ </em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><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>
+ </em></em></em></li>
+ <em><em><em> </em></em></em>
+ </ul>
+</li>
+
+<em><em><em> </em></em></em>
+<li><em><em><em><strong>Calculate</strong> </em></em></em>
+ <ul>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><strong>Sort </strong> </em></em></em>
+ <ul>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><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> </em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><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></em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><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></em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><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></em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><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>
+ </em></em></em></li>
+ <em><em><em> </em></em></em>
+ </ul>
+ <em><em><em> </em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><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
+trees</a>.</em> </em></em></em>
+ <ul>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><strong>Average Distance Using % Identity</strong></em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><strong>Neighbour Joining Using % Identity</strong></em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><strong>Average Distance Using Blosum62</strong></em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><strong>Neighbour Joining Using Blosum62<br>
+ </strong></em></em></em></li>
+ <em><em><em> </em></em></em>
+ </ul>
+ <em><em><em> <strong>Note: Since Version 2.8.1, a number of
+additional similarity measures for tree calculation are provided in
+this menu.</strong> </em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><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>
+ </em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><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>
+ </em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><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→Score menu.</em> <br>
+ </em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><strong>Autocalculate Consensus</strong><br>
+ <em>For large alignments it can be useful to deselect
+"Autocalculate Consensus" when editing. This prevents the sometimes
+lengthy calculations performed after each sequence edit.</em> <br>
+ </em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><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>
+ </em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><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></em></em></em></li>
+ <em><em><em> </em></em></em>
+ </ul>
+</li>
+
+<em><em><em> </em></em></em>
+<li><em><em><em><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> </em></em></em>
+ <ul>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><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. </em></em></em></em>
+ <ul>
+ <em><em><em><em> </em></em></em></em>
+ <li><em><em><em><em>'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> </em></em></em></em></li>
+ <em><em><em><em> </em></em></em></em>
+ <li><em><em><em><em>'Standard Databases' will check sequences
+against the EBI databases plus any active DAS sequence sources<</em></em></em></em></li>
+ <em><em><em><em> </em></em></em></em>
+ </ul>
+ <em><em><em><em> Other sub-menus allow you to pick a specific
+source to query - sources are listed alphabetically according to their
+nickname. </em><br>
+ </em></em></em></li>
+ <em><em><em> </em></em></em>
+ </ul>
+ <em><em><em> </em></em></em>
+ <p><em><em><em>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. </em></em></em></p>
+ <em><em><em> </em></em></em>
+ <ul>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><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></em></em></em></li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><strong>Secondary Structure Prediction</strong> </em></em></em>
+ <ul>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><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: </em></em></em></em>
+ <ul>
+ <em><em><em><em> </em></em></em></em>
+ <li><em><em><em><em>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.</em></em></em></em></li>
+ <em><em><em><em> </em></em></em></em>
+ <li><em><em><em><em>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.</em></em></em></em></li>
+ <em><em><em><em> </em></em></em></em>
+ <li><em><em><em><em>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). </em></em></em></em></li>
+ <em><em><em><em> </em></em></em></em>
+ </ul>
+ <em><em><em><em> </em> </em></em></em></li>
+ </ul>
+ </li>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><strong>Analysis</strong><br>
+ </em></em></em>
+ <ul>
+ <em><em><em> </em></em></em>
+ <li><em><em><em><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> </em></em></em></li>
+ <em><em><em> </em></em></em>
+ </ul>
+ </li>
+ <em><em><em> </em></em></em>
+ </ul>
+</li>
+
+<em><em><em> </em></em></em>
+</body></html>
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