+<html>\r
+<head><title>Alignment Window Menus</title></head>\r
+\r
+<body>\r
+<p><strong>Alignment Window Edit Menu</strong></p>\r
+<ul>\r
+ <li><strong>Edit</strong></li>\r
+</ul>\r
+<blockquote>\r
+ <ul>\r
+ <li><strong>Undo</strong><em><br>\r
+ This will undo any edits you make to the alignment. This applies to insertion\r
+ or deletion of gaps, cutting residues or sequences from the alignment or\r
+ pasting sequences to the current alignment or sorting the\r
+ alignment. <strong>NOTE:</strong> It DOES NOT undo colour\r
+ changes, adjustments to group sizes, or changes to the annotation panel. <br>\r
+ </em></li>\r
+ <li><strong>Redo<br>\r
+ </strong><em>Any actions which you undo can be redone using redo. <br>\r
+ </em></li>\r
+ <li><strong>Cut<br>\r
+ </strong><em>This will make a copy of the currently selected residues before\r
+ removing them from your alignment. Click on a sequence name if you wish\r
+ to select a whole sequence. <br>\r
+ Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.<br>\r
+ </em></li>\r
+ <li><strong>Copy</strong><br>\r
+ <em>Copies the currently selected residues to the system\r
+ clipboard - you can also do this by pressing <CTRL> and C\r
+ (<APPLE> and C on MacOSX). <br>\r
+ If you try to paste the clipboard contents to a text editor, you will see\r
+ the format of the copied residues is a tab separated list:<br>\r
+<pre>\r
+NAME START_RES END_RES SEQUENCE\r
+</pre><br>\r
+ </em></li>\r
+ <li><strong>Paste</strong>\r
+ <ul>\r
+ <li><strong>To New Alignment<br>\r
+ </strong><em>A new alignment window will be created from sequences previously\r
+ copied or cut to the system clipboard. <br>\r
+ Use <CTRL> and V(<APPLE> and V on MacOSX) to paste.</em></li>\r
+ <li><strong>Add To This Alignment<br>\r
+ </strong><em>Copied sequences from another alignment window can be added\r
+ to the current Jalview alignment. <br>\r
+ </em><strong> </strong></li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Delete<br>\r
+ </strong><em>This will delete the currently selected residues\r
+ without copying them to the clipboard. Like the other edit\r
+ operations, this can be undone with <strong>Undo</strong>.<br>\r
+ </em></li>\r
+ <li><strong>Select All<br>\r
+ </strong><em>Selects all the sequences and residues in the alignment. <br>\r
+ Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.<br>\r
+ </em></li>\r
+ <li><strong>Deselect All<br>\r
+ </strong><em>Removes the current selection box (red dashed box) from the\r
+ alignment window. All selected sequences, residues and marked columns will\r
+ be deselected. </em><em> <br>\r
+ Use <ESCAPE> to deselect all.<br>\r
+ </em></li>\r
+ <li><strong>Invert Selection<br>\r
+ </strong><em>Any sequence ids currently not selected will replace the current\r
+ selection. <br>\r
+ </em><strong> </strong></li>\r
+ <li><strong>Undefine Groups<br>\r
+ </strong><em>The alignment will be reset with no defined groups.<br> <strong>WARNING</strong>:\r
+ This cannot be undone.<br>\r
+ </em></li>\r
+ <li><strong>Remove Left<br>\r
+ </strong><em>If the alignment has marked columns, the alignment will be\r
+ trimmed to the left of the leftmost marked column. To mark a column, mouse\r
+ click the scale bar above the alignment. Click again to unmark a column,\r
+ or select "Deselect All" to deselect all columns.<br>\r
+ </em></li>\r
+ <li><strong>Remove Right<br>\r
+ </strong><em>If the alignment has marked columns, the alignment will be\r
+ trimmed to the left of the leftmost marked column. To mark a column, mouse\r
+ click the scale bar above the alignment. Click again to unmark a column,\r
+ or select "Deselect All" to deselect all columns.<br>\r
+ </em></li>\r
+ <li><strong>Remove Empty Columns<br>\r
+ </strong><em>All columns which only contain gap characters ("-",\r
+ ".") will be deleted.<br>\r
+ You may set the default gap character in <a href="../features/preferences.html">preferences</a>.\r
+ </em><em><br>\r
+ </em></li>\r
+ <li><strong>Remove All Gaps</strong><br>\r
+ <em><strong>All</strong> gap characters ("-", ".") will be deleted from\r
+ the alignment.<br>\r
+ You may set the default gap character in <a href="../features/preferences.html">preferences</a>.\r
+ <br>\r
+ </em> </li>\r
+ <li><strong>Remove Redundancy<br>\r
+ </strong><em>Selecting this option brings up a window asking you to select\r
+ a threshold. If the percentage identity between any two sequences\r
+ (under the current alignment) exceeds this\r
+ value then one of the sequences (the shorter) is discarded. Press the "Apply"\r
+ button to remove redundant sequences. The "Undo" button will undo the last\r
+ redundancy deletion.<br>\r
+ </em></li>\r
+ <li><strong>Pad Gaps<br>\r
+ </strong><em>Adds gaps to the end of all the sequences so they\r
+ are all the same length. This is useful for making a tree using\r
+ unaligned sequences.<br>\r
+ You may set the default gap character in <a href="../features/preferences.html">preferences</a>.\r
+ </em></li>\r
+ </ul>\r
+</blockquote>\r
+</body>\r
+</html>\r