-<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>\r
- <ul>\r
- <li><strong>Fetch Sequence</strong><br>\r
- <em>Shows a dialog window in which you can select known ids from Uniprot,\r
- EMBL, EMBLCDS or PDB database using Web Services provided by the European\r
- Bioinformatics Institute. See <a href="../features/seqfetch.html">Sequence\r
- Fetcher</a></em>.</li>\r
- <li><strong>Save As<br>\r
- </strong><em>Save the alignment to local file. A file selection window\r
- will open, use the "Files of type:" selection box to determine\r
- which <a href="../io/index.html">alignment format</a> to save as.</em></li>\r
- <li><strong>Export</strong> <em><br>\r
- Creates an alignment graphic with the current annotation, alignment background\r
- colours and group colours. If the alignment is <a\r
- href="../features/wrap.html">wrapped</a>, the output will also be wrapped\r
- and will have the same visible residue width as the open alignment. </em>\r
- <ul>\r
- <li><strong>HTML<br>\r
- </strong><em>Create a <a href="../io/export.html">web page</a>\r
- from your alignment.</em></li>\r
- <li><strong>EPS<br>\r
- </strong><em>Create an <a href="../io/export.html">Encapsulated\r
- Postscript</a> file from your alignment.</em></li>\r
- <li><strong>PNG<br>\r
- </strong><em>Create a <a href="../io/export.html">Portable Network\r
- Graphics</a> file from your alignment.</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\r
- your 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></li>\r
- </ul>\r
- </li>\r
- <li><strong>Print<br>\r
- </strong><em>Jalview will print the alignment using the current fonts\r
- and colours of your alignment. If the alignment has annotations visible,\r
- these will be printed below the alignment. If the alignment is wrapped\r
- the number of residues per line of your alignment will depend on the paper\r
- width or your alignment window width, whichever is the smaller. </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 the Newick\r
- file format, and associate them with the alignment. Note: the ids of the\r
- tree file and your alignment MUST be the same.</em></li>\r
- <li><strong>Load Features / Annotations<br>\r
- </strong><em>Load files describing precalculated <a href="../features/featuresFormat.html">sequence\r
- features</a> or <a href="../features/annotationsFormat.html">alignment\r
- annotations</a>.</em></li>\r
- <li><strong>Close<br>\r
- </strong><em>Close the alignment window. Make sure you have saved your\r
- alignment before you close - either as a Jalview project or by using the\r
- <strong>Save As</strong> menu.<br>\r
- </em></li>\r
- </ul>\r
- </li>\r
- <li><strong>Edit</strong>\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\r
- or pasting sequences to the current alignment or sorting the alignment.\r
- <strong>NOTE:</strong> It DOES NOT undo colour changes, adjustments to\r
- group sizes, or changes to the annotation panel. </em></li>\r
- <li><strong>Redo<br>\r
- </strong><em>Any actions which you undo can be redone using redo. </em></li>\r
- <li><strong>Cut<br>\r
- </strong><em>This will make a copy of the currently selected residues\r
- before removing them from your alignment. Click on a sequence name if\r
- you wish to select a whole sequence. <br>\r
- Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.</em></li>\r
- <li><strong>Copy</strong><br>\r
- <em>Copies the currently selected residues to the system clipboard - you\r
- can also do this by pressing <CTRL> and C (<APPLE> and C on\r
- MacOSX). <br>\r
- If you try to paste the clipboard contents to a text editor, you will\r
- see the format of the copied residues FASTA.</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\r
- previously 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\r
- added to the current Jalview alignment. </em></li>\r
- </ul>\r
- </li>\r
- <li><strong>Delete<br>\r
- </strong><em>This will delete the currently selected residues without\r
- copying them to the clipboard. Like the other edit operations, this can\r
- be undone with <strong>Undo</strong>.</em></li>\r
- <li><strong>Select All<br>\r
- </strong><em>Selects all the sequences and residues in the alignment.\r
- <br>\r
- Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.</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\r
- will be deselected. </em><em> <br>\r
- Use <ESCAPE> to deselect all.</em></li>\r
- <li><strong>Invert Selection<br>\r
- </strong><em>Any sequence ids currently not selected will replace the\r
- current selection. </em></li>\r
- <li><strong>Undefine Groups<br>\r
- </strong><em>The alignment will be reset with no defined groups.<br>\r
- <strong>WARNING</strong>: This cannot be undone.</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.</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.</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></li>\r
- <li><strong>Remove All Gaps</strong><br>\r
- <em>Gap characters ("-", ".") will be deleted from\r
- the selected area of the alignment. If no selection is made, ALL the gaps\r
- in the alignment will be removed.<br>\r
- You may set the default gap character in <a href="../features/preferences.html">preferences</a>.\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 (under\r
- the current alignment) exceeds this value then one of the sequences (the\r
- shorter) is discarded. Press the "Apply" button to remove redundant\r
- sequences. The "Undo" button will undo the last redundancy deletion.</em></li>\r
- <li><strong>Pad Gaps<br>\r
- </strong><em>When selected, the alignment will be kept at minimal\r
- width (so there no empty columns before or after the first or last aligned\r
- residue) and all sequences will be padded with gap characters to\r
- the before and after their terminating residues.<br>\r
- This switch is useful when making a tree using unaligned\r
- sequences and when working with alignment analysis programs which\r
- require 'properly aligned sequences' to be all the same length.<br>\r
- You may set the default for <strong>Pad Gaps</strong> in the <a href="../features/preferences.html">preferences</a>.\r
- </em></li>\r
- </em><br>\r
- </li>\r
- </ul>\r
- </li>\r
- <li><strong>Search</strong>\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\r
- alignment and create new sequence features from the queries.\r
- <br>\r
- </em></li>\r
- </ul>\r
- </li>\r
- <li><strong>View</strong>\r
- <ul>\r
- <li><strong>Font<br>\r
- </strong><em>Change the font of the display from the "Choose Font"\r
- dialog box, which is shown when this item is selected. </em></li>\r
- <li><strong>Smooth Fonts</strong><em><br>\r
- If selected, the alignment will be drawn with anti-aliasing on which looks\r
- better, but performace is reduced.\r
- </em></li>\r
- <li><strong>Wrap<br>\r
- </strong><em>When ticked, the alignment display is "<a href="../features/wrap.html">wrapped</a>"\r
- to the 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 alignment cannot\r
- be edited or have regions selected on it. </em></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</em></li>\r
- <li><strong>Boxes</strong><em><br>\r
- If this is selected the background of a residue will be coloured using\r
- the selected background colour. Useful if used in conjunction with "Colour\r
- Text." </em></li>\r
- <li><strong>Text<br>\r
- </strong><em>If this is selected the residues will be displayed using\r
- the standard 1 character amino acid alphabet.</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. </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\r
- appear as blank spaces. <br>\r
- You may set the default gap character in <a href="../features/preferences.html">preferences</a>.</em></li>\r
- <li><strong>Show Annotations<br>\r
- </strong><em>If this is selected the "Annotation Panel" will\r
- be displayed below the alignment. The default setting is to display the\r
- conservation calculation, quality calculation and consensus values as\r
- bar charts. </em></li>\r
- <li><strong>Fetch Sequence Features<br>\r
- </strong><em>If the sequence names are Swissprot entries Jalview will\r
- use the names to retrieve <a href="../features/seqfeatures.html">sequence\r
- features</a> from the EBI. Features which are 1 residue in length are\r
- coloured red, sequences longer than 1 residue are coloured blue. Move\r
- the mouse over a coloured feature to display the details of the feature.\r
- <br>\r
- Note: The retrieved information will update the sequence start and end\r
- labels if they are incorrect. </em></li>\r
- <li><strong>Show Sequence Features</strong><br><em>Show or\r
- hide sequence features on this alignment.</em></li>\r
- <li><strong>Seqence Feature Settings...</strong><em><br>\r
- <em>Control the colour and display of sequence features on the\r
- alignment. See <a\r
- href="../features/featuresettings.html">Sequence Feature Settings</a>.</em><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\r
- small window. A red box will indicate the currently visible area of the\r
- alignment. Move the visible region using the mouse. </em><strong> </strong></li>\r
- </ul>\r
- </li>\r
- <li><strong>Colour</strong>\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.</em></li>\r
- <li>Colour Scheme options: <strong>None, ClustalX, Blosum62 Score, Percentage\r
- Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity,\r
- Turn Propensity, Buried 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></li>\r
- <li><strong>By Conservation<br>\r
- </strong><em>See <a href="../colourSchemes/conservation.html">Colouring\r
- by Conservation</a>.</em></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 conservation' option\r
- appears to be doing nothing!</em></li>\r
- <li><strong>Above Identity Threshold<br>\r
- </strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage\r
- Identity</a></em><strong>.</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. <br>\r
- </em></li>\r
- <li><strong>By Annotation</strong><br>\r
- <em>Colours the alignment on a per-column value from a specified annotation.\r
- See <a href="../colourSchemes/annotationColouring.html">Annotation Colouring</a>.</em><br>\r
- </li>\r
- </ul>\r
- </li>\r
- <li><strong>Calculate</strong>\r
- <ul>\r
- <li>Sort\r
- <ul>\r
- <li><strong>by ID</strong><em><br>\r
- This will sort the sequences according to sequence name. If the sort\r
- is repeated, the order of the sorted sequences will be inverted. </em></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\r
- inverted. </em><strong></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></li>\r
- <li><em>The <a href="../calculations/sorting.html">Sort menu</a> will\r
- have some additional options if you have just done a multiple alignment\r
- calculation, or opened a tree viewer window.</em></li>\r
- </ul>\r
- </li>\r
- <li><strong>Calculate Tree </strong> <br>\r
- <em>Functions for calculating trees on the alignment or the currently\r
- 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</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\r
- alignments</a>.</em></li>\r
- <li><strong>Principal Component Analysis</strong><br>\r
- <em>Shows a spatial clustering of the sequences based on the BLOSUM62\r
- scores in the alignment. See <a href="../calculations/pca.html">Principal\r
- Component Analysis</a>.</em> </li>\r
- <li><strong>Translate cDNA</strong><br>\r
- <em>If you are viewing a cDNA alignment a very simple translation service\r
- is available. The translation ignores all gaps in the cDNA sequences.\r
- </em> <br>\r
- </li>\r
- </ul>\r
- </li>\r
- <li><strong>Web Service<br>\r
- </strong> <em>Selecting one of the following menu items starts a remote service\r
- on compute facilities at the University of Dundee. You need a continuous network\r
- connection in order to use these services through Jalview. </em>\r
- <ul>\r
- <li><strong>Alignment </strong>\r
- <ul>\r
- <li><strong>ClustalW Multiple Sequence Alignment</strong><br>\r
- <em> Submits all, or just the currently selected sequences for alignment\r
- with clustal W.</em></li>\r
- <li><strong>ClustalW Multiple Sequence Alignment Realign</strong><br>\r
- <em> Submits the alignment or currently selected region for re-alignment\r
- with clustal W. Use this if you have added some new sequences to an\r
- existing alignment.</em></li>\r
- <li><strong>Muscle Multiple Protein Sequence Alignment</strong><br>\r
- <em> Submits all, or jut the currently selected sequences for alignment\r
- using Muscle. Do not use this if you are working with nucleic acid\r
- sequences.</em></li>\r
- </ul>\r
- </li>\r
- <li><strong>Secondary Structure Prediction</strong>\r
- <ul>\r
- <li><strong>JPred Secondary Structure Prediction</strong><br>\r
- <em>Secondary structure prediction by network consensus. The behaviour\r
- of this calculation depends on the current selection: </em></li>\r
- <li><em>If nothing is selected, and the displayed sequences appear to\r
- be aligned, then a JNet prediction will be run for the first sequence\r
- in the alignment, using the current alignment. Otherwise the first\r
- sequence will be submitted for prediction. </em></li>\r
- <li><em>If just one sequence (or a region on one sequence) has been\r
- selected, it will be submitted to the automatic JNet prediction server\r
- for homolog detection and prediction. </em></li>\r
- <li><em>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 <strong>first</strong>\r
- sequence selected in the set (that is, the one that was first clicked\r
- on). </em> </li>\r
- </ul>\r
- </li>\r
- </ul>\r
- </li>\r
-</ul>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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>
+ <!-- NOTE: THIS PAGE COLLECTS TOGETHER THE INDIVIDUAL ALIGNMENT WINDOW MENU PAGES - DON"T EDIT INDIVIDUAL ENTRIES HERE! -->
+ <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>Page Setup ...</strong><br> <em>Open
+ the printing system's Page Setup dialog box, to control page
+ size, layout and orientation.</em></li>
+ <li><strong>Print (Control P)<br>
+ </strong><em>Jalview will print the alignment using the current
+ fonts and colours of your alignment. If the alignment has
+ annotations visible, these will be printed below the
+ alignment. If the alignment is wrapped the number of
+ residues per line of your alignment will depend on the paper
+ width or your alignment window width, whichever is the
+ smaller. </em></li>
+ <li><strong>Export Image</strong> <em><br>
+ Creates an alignment graphic with the current view's
+ annotation, alignment background colours and group colours.
+ If the alignment is <a href="../features/wrap.html">wrapped</a>,
+ the output will also be wrapped and will have the same
+ visible residue width as the open alignment. </em>
+ <ul>
+ <li><strong>HTML<br>
+ </strong><em>Create a <a href="../io/export.html">web page</a>
+ from your alignment.
+ </em></li>
+ <li><strong>EPS<br>
+ </strong><em>Create an <a href="../io/export.html">Encapsulated
+ Postscript</a> file from your alignment.
+ </em></li>
+ <li><strong>PNG<br>
+ </strong><em>Create a <a href="../io/export.html">Portable
+ Network Graphics</a> file from your alignment.
+ </em></li>
+ <li><strong>SVG<br>
+ </strong><em>Create a <a href="../io/export.html">Scalable
+ Vector Graphics</a> file from your alignment for embedding
+ in web pages.
+ </em></li>
+ <li><strong>BioJS<br>
+ </strong><em>Create a <a href="../io/export.html">BioJS MSA
+ Viewer HTML </a> file from your alignment.
+ </em></li>
+ </ul></li>
+ <li><strong>Export Features</strong><em><br> All
+ features visible on the alignment can be saved to file or
+ displayed in a textbox in either Jalview or GFF format</em></li>
+ <li><strong>Export Annotations</strong><em><br>
+ All annotations visible on the alignment can be saved to
+ file or displayed in a textbox in Jalview annotations
+ format. </em></li>
+ <li><strong>Load Associated Tree<br>
+ </strong><em>Jalview can <a href="../calculations/treeviewer.html">view
+ trees</a> stored in the Newick file format, and associate them
+ with the alignment. Note: the ids of the tree file and your
+ alignment MUST be the same.
+ </em></li>
+ <li><strong>Load Features / Annotations<br>
+ </strong><em>Load files describing precalculated <a
+ href="../features/featuresFormat.html"
+ >sequence features</a> or <a
+ href="../features/annotationsFormat.html"
+ >alignment annotations</a>.
+ </em></li>
+ <li><strong>Close (Control W)</strong><br> <em>Close
+ the alignment window. Make sure you have saved your
+ alignment before you close - either from the Desktop's <strong>Save
+ Project</strong> File menu option, or by using the <strong>Save
+ As</strong> menu.
+ </em></li>
+ </ul></li>
+ <li><strong>Edit</strong>
+ <ul>
+ <li><strong>Undo (Control Z)</strong><em><br>
+ This will undo any edits you make to the alignment. This
+ applies to insertion or deletion of gaps, cutting residues
+ or sequences from the alignment or pasting sequences to the
+ current alignment or sorting the alignment. <strong>NOTE:</strong>
+ It DOES NOT undo colour changes, adjustments to group sizes,
+ or changes to the annotation panel. </em></li>
+ <li><strong>Redo (Control Y)<br>
+ </strong><em>Any actions which you undo can be redone using redo. </em></li>
+ <li><strong>Cut (Control X)<br>
+ </strong><em>This will make a copy of the currently selected
+ residues before removing them from your alignment. Click on
+ a sequence name if you wish to select a whole sequence. <br>
+ Use <CTRL> and X (<APPLE> and X on MacOSX) to
+ cut.
+ </em></li>
+ <li><strong>Copy (Control C)</strong><br> <em>Copies
+ the currently selected residues to the system clipboard -
+ you can also do this by pressing <CTRL> and C
+ (<APPLE> and C on MacOSX). <br> If you try to
+ paste the clipboard contents to a text editor, you will see
+ the format of the copied residues FASTA.
+ </em></li>
+ <li><strong>Paste </strong>
+ <ul>
+ <li><strong>To New Alignment (Control Shift V)<br>
+ </strong><em>A new alignment window will be created from
+ sequences previously copied or cut to the system
+ clipboard. <br> Use <CTRL> and <SHIFT>
+ and V(<APPLE> and <SHIFT;> and and V on
+ MacOSX) to paste.
+ </em></li>
+ <li><strong>Add To This Alignment (Control V)<br>
+ </strong><em>Copied sequences from another alignment window can
+ be added to the current Jalview alignment. </em></li>
+ </ul></li>
+ <li><strong>Delete (Backspace)<br>
+ </strong><em>This will delete the currently selected residues
+ without copying them to the clipboard. Like the other edit
+ operations, this can be undone with <strong>Undo</strong>.
+ </em></li>
+ <li><strong>Remove Left (Control L)<br>
+ </strong><em>If the alignment has marked columns, the alignment will
+ be trimmed to the left of the leftmost marked column. To
+ mark a column, mouse click the scale bar above the
+ alignment. Click again to unmark a column, or select
+ "Deselect All" to deselect all columns.</em></li>
+ <li><strong>Remove Right (Control R)<br>
+ </strong><em>If the alignment has marked columns, the alignment will
+ be trimmed to the left of the leftmost marked column. To
+ mark a column, mouse click the scale bar above the
+ alignment. Click again to unmark a column, or select
+ "Deselect All" to deselect all columns.</em></li>
+ <li><strong>Remove Empty Columns (Control E)<br>
+ </strong><em>All columns which only contain gap characters
+ ("-", ".") will be deleted.<br> You
+ may set the default gap character in <a
+ href="../features/preferences.html"
+ >preferences</a>.
+ </em></li>
+ <li><strong>Remove All Gaps (Control Shift E)</strong><br>
+ <em>Gap characters ("-", ".") will be
+ deleted from the selected area of the alignment. If no
+ selection is made, ALL the gaps in the alignment will be
+ removed.<br> You may set the default gap character in <a
+ href="../features/preferences.html"
+ >preferences</a>.
+ </em></li>
+ <li><strong>Remove Redundancy (Control D)<br>
+ </strong><em>Selecting this option brings up a window asking you to
+ select a threshold. If the percentage identity between any
+ two sequences (under the current alignment) exceeds this
+ value then one of the sequences (the shorter) is discarded.
+ Press the "Apply" button to remove redundant
+ sequences. The "Undo" button will undo the last
+ redundancy deletion.</em></li>
+ <li><strong>Pad Gaps<br>
+ </strong><em>When selected, the alignment will be kept at minimal
+ width (so there are no empty columns before or after the
+ first or last aligned residue) and all sequences will be
+ padded with gap characters before and after their
+ terminating residues.<br> This switch is useful when
+ making a tree using unaligned sequences and when working
+ with alignment analysis programs which require 'properly
+ aligned sequences' to be all the same length.<br> You
+ may set the default for <strong>Pad Gaps</strong> in the <a
+ href="../features/preferences.html"
+ >preferences</a>.
+ </em></li>
+ </ul></li>
+ <li><strong>Select</strong>
+ <ul>
+ <li><a href="../features/search.html"><strong>Find...
+ (Control F)</strong></a><br> <em>Opens the Find dialog box to
+ search for residues, sequence name or residue position
+ within the alignment and create new sequence features from
+ the queries. </em>
+ <li><strong>Select All (Control A)</strong><strong><br>
+ </strong><em>Selects all the sequences and residues in the
+ alignment. <br> Use <CTRL> and A (<APPLE>
+ and A on a MacOSX) to select all.
+ </em></em></li>
+ <li><strong>Deselect All (Escape)<br>
+ </strong><em>Removes the current selection box (red dashed box) from
+ the alignment window. All selected sequences, residues and
+ marked columns will be deselected. </em><em> <br> Use
+ <ESCAPE> to deselect all.
+ </em></li>
+ <li><strong>Invert Sequence Selection (Control I)<br>
+ </strong><em>Any sequence ids currently not selected will replace
+ the current selection. </em></li>
+ <li><strong>Invert Column Selection (Control Alt
+ I)<br>
+ </strong><em>Any columns currently not selected will replace the
+ current column selection. </em></li>
+ <li><strong>Create Group (Control G)<br></strong> <em>Create
+ a group containing the currently selected sequences.</em></li>
+ <li><strong>Remove Group (Shift Control G)<br></strong>
+ <em>Ungroup the currently selected sequence group.</em></li>
+ <li><strong>Make Groups for selection<br /></strong> <em>The
+ currently selected groups of the alignment will be
+ subdivided according to the contents of the currently
+ selected region. <br />Use this to subdivide an alignment
+ based on the different combinations of residues at marked
+ columns.
+ </em></li>
+ <li><strong>Undefine Groups (Control U)<br>
+ </strong><em>The alignment will be reset with no defined groups.<br>
+ <strong>WARNING</strong>: This cannot be undone.
+ </em></li>
+ <li><strong><a
+ href="../features/columnFilterByAnnotation.html"
+ >Select/Hide Columns by Annotation</a></strong> <br /> <em>Select
+ or Hide columns in the alignment according to secondary
+ structure, labels and values shown in alignment annotation
+ rows. </em></li>
+ </ul></li>
+ <li><strong>View</strong>
+ <ul>
+ <li><strong>New View (Control T)</strong><em><br>
+ Creates a new view from the current alignment view. </em></li>
+ <li><strong>Expand Views (X)</strong><em><br>
+ Display each view associated with the alignment in its own
+ alignment window, allowing several views to be displayed
+ simultaneously. </em></li>
+ <li><strong>Gather Views (G)</strong><em><br>
+ Each view associated with the alignment will be displayed
+ within its own tab on the current alignment window. </em></li>
+ <li><strong>Show→(all Columns / Sequences /
+ Sequences and Columns)</strong><em><br> All hidden Columns
+ / Sequences / Sequences and Columns will be revealed. </em></li>
+ <li><strong>Hide→(all Columns / Sequences /
+ Selected Region / All but Selected Region )</strong><em><br>
+ Hides the all the currently selected Columns / Sequences /
+ Region or everything but the selected Region.</em></li>
+ <li><strong>Automatic Scrolling<br>
+ </strong><em>When selected, the view will automatically scroll to
+ display the highlighted sequence position corresponding to
+ the position under the mouse pointer in a linked alignment
+ or structure view.</em></li>
+ <li><strong>Show Sequence Features</strong><br> <em>Show
+ or hide sequence features on this alignment.</em></li>
+ <li><strong><a
+ href="../features/featuresettings.html"
+ >Sequence Feature Settings...</a> </strong><em><br> <em>Opens
+ the Sequence Feature Settings dialog box to control the
+ colour and display of sequence features on the alignment,
+ and configure and retrieve features from DAS annotation
+ servers.</em></li>
+ <li><strong>Sequence ID Tooltip</strong><em>
+ (application only) <br>This submenu's options allow the
+ inclusion or exclusion of non-positional sequence features
+ or database cross references from the tooltip shown when the
+ mouse hovers over the sequence ID panel.
+ </em></li>
+ <li><strong>Alignment Properties...<br />
+ </strong><em>Displays some simple statistics computed for the
+ current alignment view and any named properties defined on
+ the whole alignment.</em></li>
+ <li><strong><a href="../features/overview.html">Overview
+ Window</a><br> </strong><em>A scaled version of the alignment
+ will be displayed in a small window. A red box will indicate
+ the currently visible area of the alignment. Move the
+ visible region using the mouse. </em></li>
+ </ul></li>
+ <li><strong>Annotations</strong><em> (Since Jalview 2.8.2)</em>
+ <ul>
+ <li><strong>Show Annotations<br>
+ </strong><em>If this is selected the "Annotation Panel"
+ will be displayed below the alignment. The default setting
+ is to display the conservation calculation, quality
+ calculation and consensus values as bar charts. </em></li>
+ <li><strong>Show Alignment Related</strong><em><br>
+ Show all annotations that are for the alignment as a whole
+ (for example, Consensus, or secondary structure prediction
+ from alignment).</em></li>
+ <li><strong>Hide Alignment Related</strong><em><br>
+ Hide all annotations that are for the alignment as a whole.</em></li>
+ <li><strong>Show Sequence Related</strong><em><br>
+ Show all annotations that are for individual sequences.</em></li>
+ <li><strong>Hide Sequence Related</strong><em><br>
+ Hide all annotations that are for individual sequences.</em></li>
+ <li><em>You can also selectively show or hide
+ annotations from the <a href="./popupMenu.html">Popup</a> or
+ <a href="../features/annotation.html">Annotation</a> menus.
+ </em></li>
+ <li><strong>Sort by Sequence</strong><em><br>Sort
+ sequence-specific annotations by sequence order in the
+ alignment (and within that, by label).</em></li>
+ <li><strong>Sort by Label</strong><em><br>Sort
+ sequence-specific annotations by label (and within that, by
+ sequence order). If neither sort order is selected, no
+ sorting is applied, allowing you to make a manual ordering
+ of the annotations.</em></li>
+ <li><strong>Autocalculated Annotation<br>
+ </strong><em>Settings for the display of autocalculated annotation.</em>
+ <ul>
+ <li><strong>Show first<br></strong><em> Show
+ autocalculated annotations above sequence-specific
+ annotations. Note this also applies to other annotations
+ for the alignment, for example secondary structure
+ prediction from alignment.</em></li>
+ <li><strong>Show last<br></strong><em> Show
+ autocalculated / alignment annotations below
+ sequence-specific annotations.</em></li>
+ <li><strong>Apply to all groups<br>
+ </strong><em> When ticked, any modification to the current
+ settings will be applied to all autocalculated
+ annotation.</em></li>
+ <li><strong>Show Consensus Histogram<br>
+ </strong><em> Enable or disable the display of the histogram
+ above the consensus sequence.</em></li>
+ <li><strong>Show Consensus Logo<br>
+ </strong><em> Enable or disable the display of the Consensus
+ Logo above the consensus sequence.</em></li>
+ <li><strong>Normalise Consensus Logo<br>
+ </strong><em>When enabled, scales all logo stacks to the same
+ height, making it easier to compare symbol diversity in
+ highly variable regions.</em></li>
+ <li><strong>Group Conservation<br>
+ </strong><em> When ticked, display a conservation row for all
+ groups (only available for protein alignments).</em></li>
+ <li><strong>Group Consensus<br>
+ </strong><em> When ticked, display a consensus row for all
+ groups.</em></li>
+ </ul></li>
+ </ul></li>
+ <li><strong>Alignment Window Format Menu</strong>
+ <ul>
+ <li><strong>Font...<br>
+ </strong><em>Opens the "Choose Font" dialog box, in order
+ to change the font of the display and enable or disable
+ 'smooth fonts' (anti-aliasing) for faster alignment
+ rendering. </em></li>
+ <li><strong>Wrap<br>
+ </strong><em>When ticked, the alignment display is "<a
+ href="../features/wrap.html"
+ >wrapped</a>" to the width of the alignment window. This is
+ useful if your alignment has only a few sequences to view
+ its full width at once.
+ </em><br> Additional options for display of sequence numbering
+ and scales are also visible in wrapped layout mode:<br>
+ <ul>
+ <li><strong>Scale Above</strong><br>
+ <em> Show the alignment column position scale.</em></li>
+ <li><strong>Scale Left</strong><br>
+ <em> Show the sequence position for the first aligned
+ residue in each row in the left column of the alignment.</em></li>
+ <li><strong>Scale Right</strong><br>
+ <em> Show the sequence position for the last aligned
+ residue in each row in the right-most column of the
+ alignment.</em></li>
+ <li><strong>Show Sequence Limits<br>
+ </strong><em>If this box is selected the sequence name will have
+ the start and end position of the sequence appended to
+ the name, in the format NAME/START-END</em></li>
+ <li><strong>Right Align Sequence ID<br>
+ </strong><em>If this box is selected then the sequence names
+ displayed in the sequence label area will be aligned
+ against the left-hand edge of the alignment display,
+ rather than the left-hand edge of the alignment window.
+ </li>
+ <li><strong>Show Hidden Markers<br>
+ </strong><em>When this box is selected, positions in the
+ alignment where rows and columns are hidden will be
+ marked by blue arrows. </li>
+ <li><strong>Boxes</strong><em><br> If this is
+ selected the background of a residue will be coloured
+ using the selected background colour. Useful if used in
+ conjunction with "Colour Text." </em></li>
+ <li><strong>Text<br>
+ </strong><em>If this is selected the residues will be displayed
+ using the standard 1 character amino acid alphabet.</em></li>
+ <li><strong>Colour Text<br>
+ </strong><em>If this is selected the residues will be coloured
+ according to the background colour associated with that
+ residue. The colour is slightly darker than background
+ so the amino acid symbol remains visible. </em></li>
+ <li><strong>Show Gaps<br>
+ </strong><em>When this is selected, gap characters will be
+ displayed as "." or "-". If
+ unselected, then gap characters will appear as blank
+ spaces. <br> You may set the default gap character
+ in <a href="../features/preferences.html">preferences</a>.
+ </em></li>
+ <li><strong>Centre Annotation Labels<br>
+ </strong><em>Select this to center labels along an annotation
+ row relative to their associated column (default is off,
+ i.e. left-justified).</em></li>
+ <li><strong>Show Unconserved<br>
+ </strong><em>When this is selected, all consensus sequence
+ symbols will be rendered as a '.', highlighting
+ mutations in highly conserved alignments. </em></li>
+
+ </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>Neighbour Joining Using PAM250 </strong></li>
+ <li><strong>Neighbour Joining Using Sequence
+ Feature Similarity</strong></li>
+ <li><strong>Neighbour Joining Using Blosum62 </strong></li>
+ <li><strong>Neighbour Joining Using % Identity</strong></li>
+ <li><strong>Average Distance Using PAM250 </strong></li>
+ <li><strong>Average Distance Using Sequence
+ Feature Similarity</strong></li>
+ <li><strong>Average Distance Using Blosum62</strong></li>
+ <li><strong>Average Distance Using % Identity</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>
git://source.jalview.org / jalview.git / blobdiff