-<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/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.</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>Jalview load 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+-->
+<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> <em></em>
+ </li>
+ <li><strong>MSF</strong>
+ </li>
+ <li><strong>CLUSTAL</strong>
+ </li>
+ <li><strong>BLC</strong>
+ </li>
+ <li><strong>PIR</strong>
+ </li>
+ <li><strong>PFAM</strong>
+ </li>
+ </ul></li>
+ <li><strong>Print (Control P)<br> </strong><em>Jalview
+ will print the alignment using the current fonts and colours of
+ your alignment. If the alignment has annotations visible, these
+ will be printed below the alignment. If the alignment is wrapped
+ the number of residues per line of your alignment will depend on
+ the paper width or your alignment window width, whichever is the
+ smaller. </em>
+ </li>
+ <li><strong>Export Image</strong> <em><br> Creates an
+ alignment graphic with the current view's annotation, alignment
+ background colours and group colours. If the alignment is <a
+ href="../features/wrap.html">wrapped</a>, the output will also be
+ wrapped and will have the same visible residue width as the open
+ alignment. </em>
+ <ul>
+ <li><strong>HTML<br> </strong><em>Create a <a
+ href="../io/export.html">web page</a> from your alignment.</em>
+ </li>
+ <li><strong>EPS<br> </strong><em>Create an <a
+ href="../io/export.html">Encapsulated Postscript</a> file from
+ your alignment.</em>
+ </li>
+ <li><strong>PNG<br> </strong><em>Create a <a
+ href="../io/export.html">Portable Network Graphics</a> file from
+ your alignment.</em>
+ </li>
+ </ul></li>
+ <li><strong>Export Features</strong><em><br> All
+ features visible on the alignment can be saved to file or
+ displayed in a textbox in either Jalview or GFF format</em>
+ </li>
+ <li><strong>Export Annotations</strong><em><br> All
+ annotations visible on the alignment can be saved to file or
+ displayed in a textbox in Jalview annotations format. </em>
+ </li>
+ <li><strong>Load Associated Tree<br> </strong><em>Jalview
+ can <a href="../calculations/treeviewer.html">view trees</a>
+ stored in the Newick file format, and associate them with the
+ alignment. Note: the ids of the tree file and your alignment MUST
+ be the same.</em></li>
+ <li><strong>Load Features / Annotations<br> </strong><em>Load
+ files describing precalculated <a
+ href="../features/featuresFormat.html">sequence features</a> or <a
+ href="../features/annotationsFormat.html">alignment
+ annotations</a>.</em></li>
+ <li><strong>Close (Control W)</strong><br> <em>Close
+ the alignment window. Make sure you have saved your alignment
+ before you close - either as a Jalview project or by using the <strong>Save
+ As</strong> menu.</em>
+ </li>
+ </ul></li>
+ <li><strong>Edit</strong>
+ <ul>
+ <li><strong>Undo (Control Z)</strong><em><br> This
+ will undo any edits you make to the alignment. This applies to
+ insertion or deletion of gaps, cutting residues or sequences from
+ the alignment or pasting sequences to the current alignment or
+ sorting the alignment. <strong>NOTE:</strong> It DOES NOT undo
+ colour changes, adjustments to group sizes, or changes to the
+ annotation panel. </em>
+ </li>
+ <li><strong>Redo (Control Y)<br> </strong><em>Any
+ actions which you undo can be redone using redo. </em>
+ </li>
+ <li><strong>Cut (Control X)<br> </strong><em>This
+ will make a copy of the currently selected residues before
+ removing them from your alignment. Click on a sequence name if you
+ wish to select a whole sequence. <br> Use <CTRL> and X
+ (<APPLE> and X on MacOSX) to cut.</em>
+ </li>
+ <li><strong>Copy (Control C)</strong><br> <em>Copies
+ the currently selected residues to the system clipboard - you can
+ also do this by pressing <CTRL> and C (<APPLE> and C
+ on MacOSX). <br> If you try to paste the clipboard contents
+ to a text editor, you will see the format of the copied residues
+ FASTA.</em></li>
+ <li><strong>Paste </strong>
+ <ul>
+ <li><strong>To New Alignment (Control Shift V)<br>
+ </strong><em>A new alignment window will be created from sequences
+ previously copied or cut to the system clipboard. <br> Use
+ <CTRL> and <SHIFT> and V(<APPLE> and
+ <SHIFT;> and and V on MacOSX) to paste.</em>
+ </li>
+ <li><strong>Add To This Alignment (Control V)<br>
+ </strong><em>Copied sequences from another alignment window can be
+ added to the current Jalview alignment. </em>
+ </li>
+ </ul></li>
+ <li><strong>Delete (Backspace)<br> </strong><em>This
+ will delete the currently selected residues without copying them
+ to the clipboard. Like the other edit operations, this can be
+ undone with <strong>Undo</strong>.</em>
+ </li>
+ <li><strong>Remove Left (Control L)<br> </strong><em>If
+ the alignment has marked columns, the alignment will be trimmed to
+ the left of the leftmost marked column. To mark a column, mouse
+ click the scale bar above the alignment. Click again to unmark a
+ column, or select "Deselect All" to deselect all
+ columns.</em></li>
+ <li><strong>Remove Right (Control R)<br> </strong><em>If
+ the alignment has marked columns, the alignment will be trimmed to
+ the left of the leftmost marked column. To mark a column, mouse
+ click the scale bar above the alignment. Click again to unmark a
+ column, or select "Deselect All" to deselect all
+ columns.</em></li>
+ <li><strong>Remove Empty Columns (Control E)<br>
+ </strong><em>All columns which only contain gap characters
+ ("-", ".") will be deleted.<br> You may
+ set the default gap character in <a
+ href="../features/preferences.html">preferences</a>. </em>
+ </li>
+ <li><strong>Remove All Gaps (Control Shift E)</strong><br>
+ <em>Gap characters ("-", ".") will be
+ deleted from the selected area of the alignment. If no selection
+ is made, ALL the gaps in the alignment will be removed.<br>
+ You may set the default gap character in <a
+ href="../features/preferences.html">preferences</a>. </em>
+ </li>
+ <li><strong>Remove Redundancy (Control D)<br> </strong><em>Selecting
+ this option brings up a window asking you to select a threshold.
+ If the percentage identity between any two sequences (under the
+ current alignment) exceeds this value then one of the sequences
+ (the shorter) is discarded. Press the "Apply" button to
+ remove redundant sequences. The "Undo" button will undo
+ the last redundancy deletion.</em>
+ </li>
+ <li><strong>Pad Gaps<br> </strong><em>When selected,
+ the alignment will be kept at minimal width (so there no empty
+ columns before or after the first or last aligned residue) and all
+ sequences will be padded with gap characters to the before and
+ after their terminating residues.<br> This switch is useful
+ when making a tree using unaligned sequences and when working with
+ alignment analysis programs which require 'properly aligned
+ sequences' to be all the same length.<br> You may set the
+ default for <strong>Pad Gaps</strong> in the <a
+ href="../features/preferences.html">preferences</a>. </em>
+ </li>
+ </ul></li>
+ <li><strong>Select</strong>
+ <ul>
+ <li><strong><a href="../features/search.html">Find...
+ (Control F)</a> </strong><em><br> Opens the Find dialog box to
+ search for residues, sequence name or residue position within the
+ alignment and create new sequence features from the queries. </em>
+ </li>
+ <li><strong>Select All (Control A)<br> </strong><em>Selects
+ all the sequences and residues in the alignment. <br> Use
+ <CTRL> and A (<APPLE> and A on a MacOSX) to select
+ all.</em></li>
+ <li><strong>Deselect All (Escape)<br> </strong><em>Removes
+ the current selection box (red dashed box) from the alignment
+ window. All selected sequences, residues and marked columns will
+ be deselected. </em><em> <br> Use <ESCAPE> to deselect
+ all.</em></li>
+ <li><strong>Invert Sequence Selection (Control I)<br>
+ </strong><em>Any sequence ids currently not selected will replace the
+ current selection. </em>
+ </li>
+ <li><strong>Invert Column Selection (Control Alt I)<br>
+ </strong><em>Any columns currently not selected will replace the current
+ column selection. </em>
+ </li>
+ <li><strong>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>Make Groups<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>
+ </ul></li>
+ <li><strong>View</strong>
+ <ul>
+ <li><strong>New View (Control T)</strong><em><br>
+ Creates a new view from the current alignment view. </em>
+ </li>
+ <li><strong>Expand Views (X)</strong><em><br> Display
+ each view associated with the alignment in its own alignment
+ window, allowing several views to be displayed simultaneously. </em>
+ </li>
+ <li><strong>Gather Views (G)</strong><em><br> Each
+ view associated with the alignment will be displayed within its
+ own tab on the current alignment window. </em>
+ </li>
+ <li><strong>Show→(all Columns / Sequences /
+ Sequences and Columns)</strong><em><br> All hidden Columns /
+ Sequences / Sequences and Columns will be revealed. </em>
+ </li>
+ <li><strong>Hide→(all Columns / Sequences /
+ Selected Region / All but Selected Region )</strong><em><br>
+ Hides the all the currently selected Columns / Sequences / Region
+ or everything but the selected Region.</em>
+ </li>
+ <li><strong>Automatic Scrolling<br> </strong><em>When
+ selected, the view will automatically scroll to display the
+ highlighted sequence position corresponding to the position under
+ the mouse pointer in a linked alignment or structure view.</em></li>
+ <li><strong>Show Annotations<br> </strong><em>If this
+ is selected the "Annotation Panel" will be displayed
+ below the alignment. The default setting is to display the
+ conservation calculation, quality calculation and consensus values
+ as bar charts. </em>
+ </li>
+ <li><strong>Autocalculated Annotation<br> </strong><em>Settings
+ for the display of autocalculated annotation.</em>
+ <ul>
+ <li><strong>Apply to all groups<br> </strong><em> When
+ ticked, any modification to the current settings will be applied
+ to all autocalculated annotation.</em></li>
+ <li><strong>Show Consensus Histogram<br> </strong><em>
+ Enable or disable the display of the histogram above the
+ consensus sequence.</em></li>
+ <li><strong>Show Consensus Profile<br> </strong><em> Enable
+ or disable the display of the sequence logo above the consensus
+ sequence.</em></li>
+ <li><strong>Group Conservation<br> </strong><em> When
+ ticked, display a conservation row for all groups (only available
+ for protein alignments).</em></li>
+ <li><strong>Apply to all groups<br> </strong><em> When
+ ticked, display a consensus row for all groups.</em></li>
+ </ul></li>
+ <li><strong>Show Sequence Features</strong><br> <em>Show
+ or hide sequence features on this alignment.</em>
+ </li>
+ <li><strong><a href="../features/featuresettings.html">Seqence
+ Feature Settings...</a> </strong><em><br> <em>Opens the
+ Sequence Feature Settings dialog box to control the colour and
+ display of sequence features on the alignment, and configure and
+ retrieve features from DAS annotation servers.</em>
+ </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>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>
+ </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 the BLOSUM62 scores
+ in 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>
+ </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
+ will use 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 the sequence and retrieve all database cross
+ references and PDB ids associated with all or just the selected
+ sequences in the alignment. <br />'Standard Databases' will check
+ sequences against the EBI databases plus any active DAS sequence
+ sources, or you can verify against a specific source from one of
+ the sub-menus.</em><br></li>
+ <li><strong>Envision2 Services</strong><br /><em> Submits one or
+ more sequences, sequence IDs or database references to analysis
+ workflows provided by the <a
+ href="http://www.ebi.ac.uk/enfin-srv/envision2">EnVision2 web
+ application</a>. This allows Jalview users to easily access the EnCore
+ network of databases and analysis services developed by members of
+ <a href="http://www.enfin.org">ENFIN</a></em>.</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