+ <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