<html>\r
-<head><title>Alignment Window Menus</title></head>\r
+<head>\r
+<title>Alignment Window Menus</title>\r
+</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>Adds gaps to the end of all the sequences so they are all \r
- the same length. This is useful for making a tree using unaligned sequences.<br>\r
- You may set the default gap character in <a href="../features/preferences.html">preferences</a>. \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 alignment. \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>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>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>Seqence Settings </strong><br>\r
- <em>If features have been added to the alignment then the priority of \r
- rendering the features can be altered so that overlapping features can \r
- be displayed or hidden. See <a href="features/seqfeatures.html">Sequence \r
- Features</a>.</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
- </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
+ <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\r
+ Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by\r
+ the European Bioinformatics Institute. See <a\r
+ href="../features/seqfetch.html">Sequence Fetcher</a></em>.</li>\r
+ <li><strong>Add Sequences</strong><em><br>\r
+ Add sequences to the visible alignment from file, URL, or cut &\r
+ paste window </em></li>\r
+ <li><strong>Reload</strong><em><br>\r
+ Reloads the alignment from the original file, if available.<br>\r
+ <strong>Warning: This will delete any edits, analyses and\r
+ colourings applied since the alignment was last saved, and cannot be\r
+ undone.</strong></em></li>\r
+ <li><strong>Save (Control S)</strong><em><br>\r
+ Saves the alignment to the file it was loaded from (if available), in\r
+ the same format, updating the original in place. </em></li>\r
+ <li><strong>Save As (Control Shift S)<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\r
+ determine which <a href="../io/index.html">alignment format</a> to\r
+ save as.</em></li>\r
+ <li><strong>Output to Textbox<br>\r
+ </strong><em>The alignment will be displayed in plain text in a new\r
+ window, which you can "Copy and Paste" using the pull down\r
+ menu, or your standard operating system copy and paste keys. The\r
+ output window also has a <strong>"New Window"</strong>\r
+ button to import the (possibly edited) text as a new alignment.<br>\r
+ Select the format of the text by selecting one of the following menu\r
+ 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 (Control P)<br>\r
+ </strong><em>Jalview will print the alignment using the current fonts and\r
+ colours of your alignment. If the alignment has annotations visible,\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\r
+ paper width or your alignment window width, whichever is the smaller.\r
+ </em></li>\r
+ <li><strong>Export Image</strong> <em><br>\r
+ Creates an alignment graphic with the current view's annotation,\r
+ alignment background colours and group colours. If the alignment is <a\r
+ href="../features/wrap.html">wrapped</a>, the output will also be\r
+ wrapped and will have the same visible residue width as the open\r
+ alignment. </em>\r
+ <ul>\r
+ <li><strong>HTML<br>\r
+ </strong><em>Create a <a href="../io/export.html">web page</a> from your\r
+ 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>Export Features</strong><em><br>\r
+ All features visible on the alignment can be saved to file or\r
+ displayed in a textbox in either Jalview or GFF format</em></li>\r
+ <li><strong>Export Annotations</strong><em><br>\r
+ All annotations visible on the alignment can be saved to file or\r
+ displayed in a textbox in Jalview annotations format. </em></li>\r
+ <li><strong>Load Associated Tree<br>\r
+ </strong><em>Jalview can <a href="../calculations/treeviewer.html">view\r
+ trees</a> stored in the Newick file format, and associate them with the\r
+ alignment. Note: the ids of the tree file and your alignment MUST be\r
+ the same.</em></li>\r
+ <li><strong>Load Features / Annotations<br>\r
+ </strong><em>Load files describing precalculated <a\r
+ href="../features/featuresFormat.html">sequence features</a> or <a\r
+ href="../features/annotationsFormat.html">alignment annotations</a>.</em></li>\r
+ <li><strong>Close (Control W)</strong><br>\r
+ <em>Close the alignment window. Make sure you have saved your\r
+ alignment before you close - either as a Jalview project or by using\r
+ the <strong>Save As</strong> menu.</em></li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Edit</strong>\r
+ <ul>\r
+ <li><strong>Undo (Control Z)</strong><em><br>\r
+ This will undo any edits you make to the alignment. This applies to\r
+ insertion or deletion of gaps, cutting residues or sequences from the\r
+ alignment or pasting sequences to the current alignment or sorting the\r
+ alignment. <strong>NOTE:</strong> It DOES NOT undo colour changes,\r
+ adjustments to group sizes, or changes to the annotation panel. </em></li>\r
+ <li><strong>Redo (Control Y)<br>\r
+ </strong><em>Any actions which you undo can be redone using redo. </em></li>\r
+ <li><strong>Cut (Control X)<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 (Control C)</strong><br>\r
+ <em>Copies the currently selected residues to the system\r
+ clipboard - you can also do this by pressing <CTRL> and C\r
+ (<APPLE> and C on MacOSX). <br>\r
+ If you try to paste the clipboard contents to a text editor, you will\r
+ see the format of the copied residues FASTA.</em></li>\r
+ <li><strong>Paste </strong>\r
+ <ul>\r
+ <li><strong>To New Alignment (Control Shift V)<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 <SHIFT> and V(<APPLE> and\r
+ <SHIFT;> and and V on MacOSX) to paste.</em></li>\r
+ <li><strong>Add To This Alignment (Control V)<br>\r
+ </strong><em>Copied sequences from another alignment window can be added\r
+ to the current Jalview alignment. </em></li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Delete (Backspace)<br>\r
+ </strong><em>This will delete the currently selected residues without\r
+ copying them to the clipboard. Like the other edit operations, this\r
+ can be undone with <strong>Undo</strong>.</em></li>\r
+ <li><strong>Remove Left (Control L)<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,\r
+ mouse click the scale bar above the alignment. Click again to unmark a\r
+ column, or select "Deselect All" to deselect all columns.</em></li>\r
+ <li><strong>Remove Right (Control R)<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,\r
+ mouse click the scale bar above the alignment. Click again to unmark a\r
+ column, or select "Deselect All" to deselect all columns.</em></li>\r
+ <li><strong>Remove Empty Columns (Control E)<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\r
+ href="../features/preferences.html">preferences</a>. </em></li>\r
+ <li><strong>Remove All Gaps (Control Shift E)</strong><br>\r
+ <em>Gap characters ("-", ".") will be deleted\r
+ from the selected area of the alignment. If no selection is made, ALL\r
+ the gaps in the alignment will be removed.<br>\r
+ You may set the default gap character in <a\r
+ href="../features/preferences.html">preferences</a>. </em></li>\r
+ <li><strong>Remove Redundancy (Control D)<br>\r
+ </strong><em>Selecting this option brings up a window asking you to select\r
+ a threshold. If the percentage identity between any two sequences\r
+ (under the current alignment) exceeds this value then one of the\r
+ sequences (the shorter) is discarded. Press the "Apply"\r
+ button to remove redundant sequences. The "Undo" button will\r
+ 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 width\r
+ (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 the\r
+ before and after their terminating residues.<br>\r
+ This switch is useful when making a tree using unaligned sequences and\r
+ when working with alignment analysis programs which require 'properly\r
+ aligned sequences' to be all the same length.<br>\r
+ You may set the default for <strong>Pad Gaps</strong> in the <a\r
+ href="../features/preferences.html">preferences</a>. </em></li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Select</strong>\r
+ <ul>\r
+ <li><strong><a href="../features/search.html">Find...\r
+ (Control F)</a></strong><em><br>\r
+ Opens the Find dialog box to search for residues, sequence name or\r
+ residue position within the alignment and create new sequence features\r
+ from the queries. </em></li>\r
+ <li><strong>Select All (Control A)<br>\r
+ </strong><em>Selects all the sequences and residues in the alignment. <br>\r
+ Use <CTRL> and A (<APPLE> and A on a MacOSX) to select\r
+ all.</em></li>\r
+ <li><strong>Deselect All (Escape)<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 Sequence Selection (Control I)<br>\r
+ </strong><em>Any sequence ids currently not selected will replace the\r
+ current selection. </em></li>\r
+ <li><strong>Invert Column Selection (Control Alt I)<br>\r
+ </strong><em>Any columns currently not selected will replace the current\r
+ column selection. </em></li>\r
+ <li><strong>Undefine Groups (Control U)<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
+ </ul>\r
+ </li>\r
+ <li><strong>View</strong>\r
+ <ul>\r
+ <li><strong>New View (Control T)</strong><em><br>\r
+ Creates a new view from the current alignment view. </em></li>\r
+ <li><strong>Expand Views (X)</strong><em><br>\r
+ Display each view associated with the alignment in its own alignment\r
+ window, allowing several views to be displayed simultaneously. </em></li>\r
+ <li><strong>Gather Views (G)</strong><em><br>\r
+ Each view associated with the alignment will be displayed within its\r
+ own tab on the current alignment window. </em></li>\r
+ <li><strong>Show→(all Columns / Sequences)</strong><em><br>\r
+ All hidden Columns / Sequences will be revealed. </em></li>\r
+ <li><strong>Hide→(all Columns / Sequences)</strong><em><br>\r
+ Hides the all the currently selected Columns / Sequences</em></li>\r
+ <li><strong>Show Annotations<br>\r
+ </strong><em>If this is selected the "Annotation Panel" will be\r
+ displayed below the alignment. The default setting is to display the\r
+ conservation calculation, quality calculation and consensus values as\r
+ bar charts. </em></li>\r
+ <li><strong>Show Sequence Features</strong><br>\r
+ <em>Show or hide sequence features on this alignment.</em></li>\r
+ <li><strong><a href="../features/featuresettings.html">Seqence\r
+ Feature Settings...</a></strong><em><br>\r
+ <em>Opens the Sequence Feature Settings dialog box to control the\r
+ colour and display of sequence features on the alignment, and\r
+ configure and retrieve features from DAS annotation servers.</em></li>\r
+ <li><strong><a href="../features/overview.html">Overview\r
+ 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\r
+ the alignment. Move the visible region using the mouse. </em></li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Alignment Window Format Menu</strong>\r
+ <ul>\r
+ <li><strong>Font...<br>\r
+ </strong><em>Opens the "Choose Font" dialog box, in order to\r
+ change the font of the display and enable or disable 'smooth fonts'\r
+ (anti-aliasing) for faster alignment rendering. </em></li>\r
+ <li><strong>Wrap<br>\r
+ </strong><em>When ticked, the alignment display is "<a\r
+ href="../features/wrap.html">wrapped</a>" to the width of the\r
+ alignment window. This is useful if your alignment has only a few\r
+ sequences to view its full width at once.<br>\r
+ Additional options for display of sequence numbering and scales are\r
+ also visible in wrapped layout mode:<br>\r
+ <ul>\r
+ <li><strong>Scale Above</strong><br>\r
+ Show the alignment column position scale.</li>\r
+ <li><strong>Scale Left</strong><br>\r
+ Show the sequence position for the first aligned residue in each row\r
+ in the left column of the alignment.</li>\r
+ <li><strong>Scale Right</strong><br>\r
+ Show the sequence position for the last aligned residue in each row\r
+ in the right-most column of the alignment.</li>\r
+ <li><strong>Show Sequence Limits<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\r
+ NAME/START-END</em></li>\r
+ <li><strong>Right Align Sequence ID<br>\r
+ </strong><em>If this box is selected then the sequence names displayed in\r
+ the sequence label area will be aligned against the left-hand edge of\r
+ the alignment display, rather than the left-hand edge of the alignment\r
+ window.</li>\r
+ <li><strong>Show Hidden Markers<br>\r
+ </strong><em>When this box is selected, positions in the alignment where\r
+ rows and columns are hidden will be marked by blue arrows.</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\r
+ "Colour Text." </em></li>\r
+ <li><strong>Text<br>\r
+ </strong><em>If this is selected the residues will be displayed using the\r
+ standard 1 character amino acid alphabet.</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\r
+ slightly darker than background so the amino acid symbol remains\r
+ 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\r
+ will appear as blank spaces. <br>\r
+ You may set the default gap character in <a\r
+ href="../features/preferences.html">preferences</a>.</em></li>\r
+ </ul>\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\r
+ colour will be applied to all currently defined groups.<br>\r
+ </em></li>\r
+ <li><strong><a href="../colourSchemes/textcolour.html">Colour\r
+ Text...</a></strong><em><br>\r
+ Opens the Colour Text dialog box to set a different text colour for\r
+ light and dark background, and the intensity threshold for transition\r
+ between them. </em></li>\r
+ <li>Colour Scheme options: <strong>None, ClustalX,\r
+ Blosum62 Score, Percentage Identity, Zappo, Taylor, Hydrophobicity,\r
+ Helix Propensity, Strand Propensity, Turn Propensity, Buried Index,\r
+ Nucleotide, User Defined<br>\r
+ </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for a\r
+ description of all colour schemes.</em><br>\r
+ </li>\r
+ <li><strong>By Conservation<br>\r
+ </strong><em>See <a href="../colourSchemes/conservation.html">Colouring\r
+ by Conservation</a>.</em><br>\r
+ </li>\r
+ <li><strong>Modify Conservation Threshold<br>\r
+ </strong><em>Use this to display the conservation threshold slider window.\r
+ Useful if the window has been closed, or if the 'by conservation'\r
+ option appears to be doing nothing!</em><br>\r
+ </li>\r
+ <li><strong>Above Identity Threshold<br>\r
+ </strong><em>See <a href="../colourSchemes/abovePID.html">Above\r
+ Percentage Identity</a></em><strong>.<br>\r
+ </strong></li>\r
+ <li><strong>Modify Identity Threshold<br>\r
+ </strong><em>Use this to set the threshold value for colouring above\r
+ Identity. 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\r
+ annotation. See <a href="../colourSchemes/annotationColouring.html">Annotation\r
+ Colouring</a>.</em><br>\r
+ </li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Calculate</strong>\r
+ <ul>\r
+ <li><strong>Sort </strong>\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. If\r
+ 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\r
+ menu</a> will have some additional options if you have just done a\r
+ multiple alignment calculation, or opened a tree viewer window.</em><br>\r
+ </li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Calculate Tree </strong> <br>\r
+ <em>Functions for calculating trees on the alignment or the\r
+ currently selected region. See <a href="../calculations/tree.html">calculating\r
+ trees</a>.</em>\r
+ <ul>\r
+ <li><strong>Average Distance Using % Identity</strong></li>\r
+ <li><strong>Neighbour Joining Using % Identity</strong></li>\r
+ <li><strong>Average Distance Using Blosum62</strong></li>\r
+ <li><strong>Neighbour Joining Using Blosum62<br>\r
+ </strong></li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Pairwise Alignments</strong><br>\r
+ <em>Applies Smith and Waterman algorithm to selected sequences.\r
+ See <a href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>\r
+ </li>\r
+ <li><strong>Principal Component Analysis</strong><br>\r
+ <em>Shows a spatial clustering of the sequences based on the\r
+ BLOSUM62 scores in the alignment. See <a\r
+ href="../calculations/pca.html">Principal Component Analysis</a>.</em> <br>\r
+ </li>\r
+ <li><strong>Autocalculate Consensus</strong><br>\r
+ <em>For large alignments it can be useful to deselect\r
+ "Autocalculate Consensus" when editing. This prevents the\r
+ sometimes lengthy calculations performed after each sequence edit.</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\r
+ service on compute facilities at the University of Dundee. You need a\r
+ continuous network connection in order to use these services through\r
+ 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\r
+ alignment with clustal W.</em></li>\r
+ <li><strong>ClustalW Multiple Sequence Alignment\r
+ Realign</strong><br>\r
+ <em> Submits the alignment or currently selected region for\r
+ re-alignment with clustal W. Use this if you have added some new\r
+ sequences to an existing alignment.</em></li>\r
+ <li><strong>MAFFT Multiple Sequence Alignment</strong><br>\r
+ <em>Submits all, or just the currently selected region for\r
+ alignment with MAFFT. </em></li>\r
+ <li><strong>Muscle Multiple Protein Sequence Alignment</strong><br>\r
+ <em> Submits all, or just the currently selected sequences for\r
+ alignment using Muscle. Do not use this if you are working with\r
+ nucleic acid 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\r
+ behaviour of this calculation depends on the current selection: </em></li>\r
+ <li><em>If nothing is selected, and the displayed sequences\r
+ appear to be aligned, then a JNet prediction will be run for the\r
+ first sequence in the alignment, using the current alignment.\r
+ Otherwise the first sequence will be submitted for prediction. </em></li>\r
+ <li><em>If just one sequence (or a region on one sequence)\r
+ has been selected, it will be submitted to the automatic JNet\r
+ prediction server for homolog detection and prediction. </em></li>\r
+ <li><em>If a set of sequences are selected, and they appear\r
+ to be aligned, then the alignment will be used for a Jnet prediction\r
+ on the <strong>first</strong> sequence in the set (that is, the one\r
+ that appears first in the alignment window). </em></li>\r
+ </ul>\r
+ </li>\r
+ </ul>\r
+ </li>\r
</ul>\r
</body>\r
</html>\r
git://source.jalview.org / jalview.git / blobdiff