+<html>\r
+<head><title>Menus</title></head>\r
+\r
+<body>\r
+<p><strong>Alignment Menu</strong></p>\r
+<ul>\r
+ <li><strong>File</strong></li>\r
+ <ul>\r
+ <li><strong>Save As<br>\r
+ </strong><em>Save the alignment to local file. A file selection window will \r
+ open, use the "Files of type:" selection box to determine which \r
+ <a href="../io/index.html">alignment format</a> to save as.<br>\r
+ </em></li>\r
+ <li><strong>Export</strong> <em><br>\r
+ Creates an alignment output maintaining the alignment background colours \r
+ and group colours. If the alignment is wrapped, the output will also be \r
+ wrapped and will have the same visible residue width as the open alignment. \r
+ </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 your \r
+ 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<br>\r
+ </strong></li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Print<br>\r
+ </strong><em>Jalview will print the alignment using the current fonts and \r
+ coloursof your alignment. If the alignment has annotations visible, these \r
+ will be printed below the alignment. If the alignment is wrapped the number \r
+ of residues per line of your alignment will depend on the paper width or \r
+ your alignment window width, whichever is the smaller. </em></li>\r
+ <li><strong>Load Associated Tree<br>\r
+ </strong><em>Jalview can load in trees which are in the Newick file format \r
+ and associate them with a particular alignment. Note: the ids of the tree \r
+ file and your alignment MUST be the same.</em></li>\r
+ <li><strong>Close<br>\r
+ </strong><em>Close the alignment window. Be aware that changes to your alignment \r
+ will not be save unless specifically actioned from the "Save As" \r
+ menu.<br>\r
+ </em></li>\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, pasting \r
+ </em></li>\r
+ <li><strong>Redo<br>\r
+ </strong></li>\r
+ <li><strong>Cut</strong></li>\r
+ <li><strong>Copy</strong></li>\r
+ <li><strong>Paste </strong> \r
+ <ul>\r
+ <li><strong>To New Alignment</strong></li>\r
+ <li><strong>Add To This Alignment</strong></li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Delete</strong></li>\r
+ <li><strong>Select All</strong></li>\r
+ <li><strong>Deselect All</strong></li>\r
+ <li><strong>Invert Selection</strong></li>\r
+ <li><strong>Undefine Groups</strong></li>\r
+ <li><strong>Remove Left</strong></li>\r
+ <li><strong>Remove Right</strong></li>\r
+ <li><strong>Remove Empty Columns</strong></li>\r
+ <li><strong>Remove All Gaps</strong></li>\r
+ <li><strong>Remove Redundancy</strong></li>\r
+ <li><strong>Pad Gaps</strong></li>\r
+ </ul>\r
+</blockquote>\r
+<ul>\r
+ <li><strong>Search</strong></li>\r
+</ul>\r
+<blockquote>\r
+ <ul>\r
+ <li><strong>Find</strong></li>\r
+ </ul>\r
+</blockquote>\r
+<ul>\r
+ <li><strong>View</strong></li>\r
+</ul>\r
+<blockquote> \r
+ <ul>\r
+ <li><strong>Font</strong></li>\r
+ <li><strong>Wrap</strong></li>\r
+ <li><strong>Show Full Sequence ID</strong></li>\r
+ <li><strong>Boxes</strong></li>\r
+ <li><strong>Text</strong></li>\r
+ <li><strong>Colour Text</strong></li>\r
+ <li><strong>Show Gaps</strong></li>\r
+ <li><strong>Show Annotations</strong></li>\r
+ <li><strong>Sequence Features</strong></li>\r
+ <li><strong>Overview Window</strong></li>\r
+ </ul>\r
+</blockquote>\r
+<ul>\r
+ <li><strong>Colour</strong></li>\r
+</ul>\r
+<blockquote> \r
+ <ul>\r
+ <li><strong>Apply Colour To All Groups</strong></li>\r
+ <li><strong>None</strong></li>\r
+ <li><strong>ClustalX</strong></li>\r
+ <li><strong>Blosum62 Score</strong></li>\r
+ <li><strong>Percentage Identity</strong></li>\r
+ <li><strong>Zappo</strong></li>\r
+ <li><strong>Taylor</strong></li>\r
+ <li><strong>Hydrophobicity</strong></li>\r
+ <li><strong>Helix Propensity</strong></li>\r
+ <li><strong>Strand Propensity</strong></li>\r
+ <li><strong>Turn Propensity</strong></li>\r
+ <li><strong>Buried Index</strong></li>\r
+ <li><strong>Nucleotide</strong></li>\r
+ <li><strong>User Defined</strong></li>\r
+ <li><strong>By Conservation</strong></li>\r
+ <li><strong>Modify Conservation Threshold</strong></li>\r
+ <li><strong>Above Identity Threshold</strong></li>\r
+ <li><strong>Modify Identity Threshold</strong></li>\r
+ </ul>\r
+</blockquote>\r
+<ul>\r
+ <li><strong>Calculate</strong></li>\r
+</ul>\r
+<blockquote> \r
+ <ul>\r
+ <li><strong>Sort </strong> \r
+ <ul>\r
+ <li><strong>by ID</strong></li>\r
+ <li><strong>by Group</strong></li>\r
+ <li><strong>by Pairwise Identity</strong></li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Calculate Tree </strong> \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>Paiwise Alignments</strong></li>\r
+ <li><strong>Principal Component Analysis</strong></li>\r
+ <li><strong>Web Service </strong> \r
+ <ul>\r
+ <li><strong>Clustal Alignment</strong></li>\r
+ <li><strong>JPred</strong></li>\r
+ <li><strong>Muscle Alignment</strong></li>\r
+ </ul>\r
+ </li>\r
+ </ul>\r
+ <p> </p>\r
+</blockquote>\r
+</body>\r
+</html>\r