-<html>\r
-<head><title>Alignment Window Menus</title></head>\r
-\r
-<body>\r
-<p><strong>Alignment Window Menus</strong></p>\r
-<ul>\r
- <li><strong>File</strong></li>\r
- <ul>\r
- <li><strong>Save As<br>\r
- </strong><em>Save the alignment to local file. A file selection window will\r
- open, use the "Files of type:" selection box to determine which\r
- <a href="../io/index.html">alignment format</a> to save as.<br>\r
- </em></li>\r
- <li><strong>Export</strong> <em><br>\r
- Creates an alignment graphic with the current annotation,\r
- alignment background colours and group colours. If the alignment is <a\r
- href="../features/wrap.html">wrapped</a>, the output will also\r
- be wrapped and will have the same visible residue width as the\r
- open alignment. \r
- </em>\r
- <ul>\r
- <li><strong>HTML<br>\r
- </strong><em>Create a <a href="../io/index.html#export">web page</a>\r
- from your alignment.</em></li>\r
- <li><strong>EPS<br>\r
- </strong><em>Create an <a href="../io/index.html#export">Encapsulated\r
- Postscript</a> file from your alignment.</em></li>\r
- <li><strong>PNG<br>\r
- </strong><em>Create a <a href="../io/index.html#export">Portable Network\r
- Graphics</a> file from your alignment.<br>\r
- </em></li>\r
- </ul>\r
- </li>\r
- <li><strong>Output to Textbox<br>\r
- </strong><em>The alignment will be displayed in plain text in a new window\r
- which you can "Copy and Paste" using the pull down menu, or your\r
- standard operating system copy and paste keys. <br>\r
- Select the format of the text by selecting one of the following menu items.</em>\r
- <ul>\r
- <li><strong>FASTA</strong> <em></em></li>\r
- <li><strong>MSF</strong></li>\r
- <li><strong>CLUSTAL</strong></li>\r
- <li><strong>BLC</strong></li>\r
- <li><strong>PIR</strong></li>\r
- <li><strong>PFAM</strong><br></li>\r
- </ul>\r
- </li>\r
- <li><strong>Print<br>\r
- </strong><em>Jalview will print the alignment using the current fonts and\r
- colours of your alignment. If the alignment has annotations visible, these\r
- will be printed below the alignment. If the alignment is wrapped the number\r
- of residues per line of your alignment will depend on the paper width or\r
- your alignment window width, whichever is the smaller. <br>\r
- </em></li>\r
- <li><strong>Load Associated Tree<br>\r
- </strong><em>Jalview can <a\r
- href="../calculations/treeviewer.html">view trees</a> stored in\r
- the Newick file format, and associate them with the\r
- alignment. Note: the ids of the tree file and your alignment\r
- MUST be the same.<br>\r
- </em></li>\r
- <li><strong>Close<br>\r
- </strong><em>Close the alignment window. Make sure you have\r
- saved your alignment before you close - either as a Jalview\r
- project or by using the <strong>Save As</strong> menu.<br>\r
- </em></li>\r
- </ul>\r
- <li><strong>Edit</strong></li>\r
-</ul>\r
-<blockquote>\r
- <ul>\r
- <li><strong>Undo</strong><em><br>\r
- This will undo any edits you make to the alignment. This applies to insertion\r
- or deletion of gaps, cutting residues or sequences from the alignment or\r
- pasting sequences to the current alignment or sorting the\r
- alignment. <strong>NOTE:</strong> It DOES NOT undo colour\r
- changes, adjustments to group sizes, or changes to the annotation panel. <br>\r
- </em></li>\r
- <li><strong>Redo<br>\r
- </strong><em>Any actions which you undo can be redone using redo. <br>\r
- </em></li>\r
- <li><strong>Cut<br>\r
- </strong><em>This will make a copy of the currently selected residues before\r
- removing them from your alignment. Click on a sequence name if you wish\r
- to select a whole sequence. <br>\r
- Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.<br>\r
- </em></li>\r
- <li><strong>Copy</strong><br>\r
- <em>Copies the currently selected residues to the system\r
- clipboard - you can also do this by pressing <CTRL> and C\r
- (<APPLE> and C on MacOSX). <br>\r
- If you try to paste the clipboard contents to a text editor, you will see\r
- the format of the copied residues is a tab separated list:<br>\r
-<pre>\r
-NAME START_RES END_RES SEQUENCE\r
-</pre><br>\r
- </em></li>\r
- <li><strong>Paste </strong>\r
- <ul>\r
- <li><strong>To New Alignment<br>\r
- </strong><em>A new alignment window will be created from sequences previously\r
- copied or cut to the system clipboard. <br>\r
- Use <CTRL> and V(<APPLE> and V on MacOSX) to paste.</em></li>\r
- <li><strong>Add To This Alignment<br>\r
- </strong><em>Copied sequences from another alignment window can be added\r
- to the current Jalview alignment. <br>\r
- </em><strong> </strong></li>\r
- </ul>\r
- </li>\r
- <li><strong>Delete<br>\r
- </strong><em>This will delete the currently selected residues\r
- without copying them to the clipboard. Like the other edit\r
- operations, this can be undone with <strong>Undo</strong>.<br>\r
- </em></li>\r
- <li><strong>Select All<br>\r
- </strong><em>Selects all the sequences and residues in the alignment. <br>\r
- Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.<br>\r
- </em></li>\r
- <li><strong>Deselect All<br>\r
- </strong><em>Removes the current selection box (red dashed box) from the\r
- alignment window. All selected sequences, residues and marked columns will\r
- be deselected. </em><em> <br>\r
- Use <ESCAPE> to deselect all.<br>\r
- </em></li>\r
- <li><strong>Invert Selection<br>\r
- </strong><em>Any sequence ids currently not selected will replace the current\r
- selection. <br>\r
- </em><strong> </strong></li>\r
- <li><strong>Undefine Groups<br>\r
- </strong><em>The alignment will be reset with no defined groups.<br> <strong>WARNING</strong>:\r
- This cannot be undone.<br>\r
- </em></li>\r
- <li><strong>Remove Left<br>\r
- </strong><em>If the alignment has marked columns, the alignment will be\r
- trimmed to the left of the leftmost marked column. To mark a column, mouse\r
- click the scale bar above the alignment. Click again to unmark a column,\r
- or select "Deselect All" to deselect all columns.<br>\r
- </em></li>\r
- <li><strong>Remove Right<br>\r
- </strong><em>If the alignment has marked columns, the alignment will be\r
- trimmed to the left of the leftmost marked column. To mark a column, mouse\r
- click the scale bar above the alignment. Click again to unmark a column,\r
- or select "Deselect All" to deselect all columns.<br>\r
- </em></li>\r
- <li><strong>Remove Empty Columns<br>\r
- </strong><em>All columns which only contain gap characters ("-",\r
- ".") will be deleted.<br>\r
- You may set the default gap character in <a href="../features/preferences.html">preferences</a>.\r
- </em><em><br>\r
- </em></li>\r
- <li><strong>Remove All Gaps</strong><br>\r
- <em><strong>All</strong> gap characters ("-", ".") will be deleted from\r
- the alignment.<br>\r
- You may set the default gap character in <a href="../features/preferences.html">preferences</a>.\r
- <br>\r
- </em> </li>\r
- <li><strong>Remove Redundancy<br>\r
- </strong><em>Selecting this option brings up a window asking you to select\r
- a threshold. If the percentage identity between any two sequences\r
- (under the current alignment) exceeds this\r
- value then one of the sequences (the shorter) is discarded. Press the "Apply"\r
- button to remove redundant sequences. The "Undo" button will undo the last\r
- redundancy deletion.<br>\r
- </em></li>\r
- <li><strong>Pad Gaps<br>\r
- </strong><em>Adds gaps to the end of all the sequences so they\r
- are all the same length. This is useful for making a tree using\r
- unaligned sequences.<br>\r
- You may set the default gap character in <a href="../features/preferences.html">preferences</a>.\r
- </em></li>\r
- </ul>\r
-</blockquote>\r
-<ul>\r
- <li><strong>Search</strong></li>\r
-</ul>\r
-<blockquote>\r
- <ul>\r
- <li><strong>Find<br>\r
- </strong><em>Select this to <a href="../features/search.html">search</a>\r
- for residues, sequence name or residue position within the alignment. </em></li>\r
- </ul>\r
-</blockquote>\r
-<ul>\r
- <li><strong>View</strong></li>\r
-</ul>\r
-<blockquote>\r
- <ul>\r
- <li><strong>Font<br>\r
- </strong><em>Change the font of the display from the\r
- "Choose Font" dialog box, which is shown when this\r
- item is selected. <br>\r
- </em></li>\r
- <li><strong>Wrap<br>\r
- </strong><em>When ticked, the alignment display is\r
- "<a href="../features/wrap.html">wrapped</a>" to the\r
- width of the alignment window. This is useful if your alignment\r
- has only a few sequences to view its full width at once.<br>\r
- Options are available to show the residue numbering at the start and/or\r
- end of an alignment as well as showing the alignment position above each\r
- sequence row. <br>\r
- <strong>NOTE</strong>: When in wrapped alignment view, the\r
- alignment cannot be edited or have regions selected on it. <br>\r
- </em><strong> </strong></li>\r
- <li><strong>Show Full Sequence ID<br>\r
- </strong><em>If this box is selected the sequence name will have the start\r
- and end position of the sequence appended to the name, in the format NAME/START-END<br>\r
- </em></li>\r
- <li><strong>Boxes</strong><em><br>\r
- If this is selected the background of a residue will be coloured using the\r
- selected background colour. Useful if used in conjunction with "Colour\r
- Text." <br>\r
- </em></li>\r
- <li><strong>Text<br>\r
- </strong><em>If this is selected the residues will be displayed using the\r
- standard 1 character amino acid alphabet.<br>\r
- </em></li>\r
- <li><strong>Colour Text<br>\r
- </strong><em>If this is selected the residues will be coloured according\r
- to the background colour associated with that residue. The colour is slightly\r
- darker than background so the amino acid symbol remains visible. <br>\r
- </em></li>\r
- <li><strong>Show Gaps<br>\r
- </strong><em>When this is selected, gap characters will be displayed as "."\r
- or "-". If unselected, then gap characters will appear as blank spaces.\r
- <br>\r
- You may set the default gap character in <a href="../features/preferences.html">preferences</a>.<br>\r
- </em></li>\r
- <li><strong>Show Annotations<br>\r
- </strong><em>If this is selected the "Annotation Panel" will be\r
- displayed below the alignment. The default setting is to display the conservation\r
- calculation, quality calculation and consensus values as bar charts. </em><br>\r
- </li>\r
- <li><strong>Sequence Features<br>\r
- </strong><em>If the sequence names are Swissprot entries Jalview will use\r
- the names to retrieve <a href="../features/seqfeatures.html">sequence features</a> from the EBI. Features which are\r
- 1 residue in length are coloured red, sequences longer than 1 residue are\r
- coloured blue. Move the mouse over a coloured feature to display the details\r
- of the feature. <br>\r
- Note: The retrieved information will update the sequence start and end labels\r
- if they are incorrect. <br>\r
- </em></li>\r
- <li><strong><a href="../features/overview.html">Overview Window</a><br>\r
- </strong><em>A scaled version of the alignment will be displayed in a small\r
- window. A red box will indicate the currently visible area of the alignment.\r
- Move the visible region using the mouse. </em><strong> </strong></li>\r
- </ul>\r
-</blockquote>\r
-<ul>\r
- <li><strong>Colour</strong></li>\r
-</ul>\r
-<blockquote>\r
- <ul>\r
- <li><strong>Apply Colour To All Groups<br>\r
- </strong><em>If this is selected, any changes made to the background colour\r
- will be applied to all currently defined groups.<br>\r
- </em></li>\r
- <li>Colour Scheme options: <strong>None, ClustalX, Blosum62 Score, Percentage Identity, Zappo, Taylor,\r
- Hydrophobicity, Helix Propensity, Strand Propensity, Turn Propensity, Buried\r
- Index, Nucleotide, User Defined<br>\r
- </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for\r
- a description of all colour schemes.</em><br>\r
- </li>\r
- <li><strong>By Conservation<br>\r
- </strong><em>See <a href="../colourSchemes/conservation.html">Colouring\r
- by Conservation</a>.</em><br>\r
- </li>\r
- <li><strong>Modify Conservation Threshold<br>\r
- </strong><em>Use this to display the conservation threshold slider window.\r
- Useful if the window has been closed, or if the 'by\r
- conservation' option appears to be doing nothing!</em><br></li>\r
- <li><strong>Above Identity Threshold<br>\r
- </strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage\r
- Identity</a></em><strong>.<br>\r
- </strong></li>\r
- <li><strong>Modify Identity Threshold<br>\r
- </strong><em>Use this to set the threshold value for colouring above Identity.\r
- Useful if the window has been closed. </em></li>\r
- </ul>\r
-</blockquote>\r
-<ul>\r
- <li><strong>Calculate</strong></li>\r
-</ul>\r
-<blockquote>\r
- <ul>\r
- <li><strong>Sort </strong>\r
- <ul>\r
- <li><strong>by ID<br>\r
- </strong><em>This will sort the sequences according to sequence name.\r
- If the sort is repeated, the order of the sorted sequences will be inverted.\r
- </em><strong><br>\r
- </strong></li>\r
- <li><strong>by Group</strong><strong><br>\r
- </strong><em>This will sort the sequences according to sequence name.\r
- If the sort is repeated, the order of the sorted sequences will be inverted.\r
- </em><strong></strong><strong><br>\r
- </strong></li>\r
- <li><strong>by Pairwise Identity<br>\r
- </strong><em>This will sort the selected sequences by their percentage\r
- identity to the consensus sequence. The most similar sequence is put\r
- at the top. </em><strong><br>\r
- </strong></li>\r
- </ul>\r
- <em>The <a href="../calculations/sorting.html">Sort menu</a> will\r
- have some additional options if you have just done a multiple\r
- alignment calculation, or opened a tree viewer window.</em><br>\r
- </li>\r
- <li><strong>Calculate Tree </strong>\r
- <br><em>Functions for calculating trees on the alignment or the\r
- currently selected region. See <a\r
- href="../calculations/tree.html">calculating trees</a>.</em>\r
- <ul>\r
- <li><strong>Average Distance Using % Identity</strong></li>\r
- <li><strong>Neighbour Joining Using % Identity</strong></li>\r
- <li><strong>Average Distance Using Blosum62</strong></li>\r
- <li><strong>Neighbour Joining Using Blosum62<br></strong></li>\r
- </ul>\r
- </li>\r
- <li><strong>Pairwise Alignments</strong><br>\r
- <em>Applies Smith and Waterman algorithm to selected sequences. See <a href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>\r
- </li>\r
- <li><strong>Principal Component Analysis</strong><br>\r
- <em>Shows a spatial clustering of the sequences based on the\r
- BLOSUM62 scores in the alignment. See <a href="../calculations/pca.html">Principal Component Analysis</a>.</em>\r
- <br>\r
- </li>\r
- <li><strong>Web Service<br>\r
- </strong>\r
- <em>Selecting one of the following menu items starts a remote service\r
- on compute facilities at the University of Dundee. You need a\r
- continuous network connection in order to use these services\r
- through Jalview.\r
- </em>\r
- <ul>\r
- <li><strong>Clustal Alignment</strong><br><em>\r
- Submits all, or just the currently selected sequences for alignment with clustal W.</em><br></li>\r
- <li><strong>Clustal Realign</strong><br><em>\r
- Submits the alignment or currently selected region for\r
- re-alignment with clustal W. Use this if you have added some\r
- new sequences to an existing alignment.</em><br></li>\r
- <li><strong>Muscle Alignment</strong><br><em>\r
- Submits all, or jut the currently selected sequences for\r
- alignment using Muscle. Do not use this if you are working with\r
- nucleic acid sequences.</em><br>\r
- <li><strong>JPred</strong><br><em>\r
- Secondary structure prediction by network consensus. The\r
- behaviour of this calculation depends on the current selection:\r
- <ul>\r
- <li>If nothing is selected, and the displayed sequences appear to\r
- be aligned, then a JNet prediction will be run for the first\r
- sequence in the alignment, using the current\r
- alignment. Otherwise the first sequence will be submitted for prediction.\r
- </li>\r
- <li>If\r
- just one sequence (or a region on one sequence) has been selected,\r
- it will be submitted to the automatic JNet prediction server\r
- for homolog detection and prediction.\r
- </li>\r
-<li>If a set of sequences are selected, and they appear to be aligned,\r
-then the alignment will be used for a Jnet prediction on the\r
-<strong>first</strong> sequence selected in the set (that is, the one\r
-that was first clicked on).\r
-</li>\r
- \r
-</ul>\r
- </li>\r
- </ul>\r
- <p> </p>\r
-</blockquote>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Alignment Window Menus</title>
+</head>
+
+<body>
+ <p>
+ <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 &
+ 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>
+ <li><strong>JSON</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>
+ </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>
+
+ </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>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>
+ <ul>
+ <li><strong>Average Distance Using % Identity</strong></li>
+ <li><strong>Neighbour Joining Using % Identity</strong></li>
+ <li><strong>Average Distance Using Blosum62</strong></li>
+ <li><strong>Neighbour Joining Using Blosum62<br>
+ </strong></li>
+ </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→Score menu.</em> <br>
+ </li>
+ <li><strong>Autocalculate Consensus</strong><br> <em>For
+ large alignments it can be useful to deselect "Autocalculate
+ Consensus" when editing. This prevents the sometimes lengthy
+ 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.
+ <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>
+
+</body>
+</html>