-<tocitem text="Menus" expand="true" >\r
- <tocitem text="File" target="home"/>\r
- <tocitem text="Edit" target="home"/>\r
- <tocitem text="Font" target="home"/>\r
- <tocitem text="View" target="home"/>\r
- <tocitem text="Colour" target="colours">\r
+<tocitem text="Jalview Documentation" target="home" expand="true" >\r
+ <tocitem text="What's new" target="new" expand="false">\r
+ <tocitem text="DAS Feature Fetching" target="das.settings"/>\r
+ <tocitem text="Hide Regions" target="hiddenRegions"/>\r
+ <tocitem text="Tree/PCA Input Data" target="recoverInputdata"/>\r
+ <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>\r
+ <tocitem text="MAFFT Alignment" target="mafft"/>\r
+ </tocitem>\r
+ <tocitem text="Release History" target="release"/>\r
+ <tocitem text="Editing Alignments" target ="edit"/> \r
+ <tocitem text="Cursor Mode" target="cursor"/>\r
+ <tocitem text="Key Strokes" target="keys"/>\r
+ <tocitem text="Input / Output" target="io"/>\r
+ <tocitem text="Making figures" target="export"/>\r
+ <tocitem text="Hidden Regions" target="hiddenRegions"/>\r
+ <tocitem text="Viewing PDB Files" target="viewingpdbs"/>\r
+ <tocitem text="Sequence Features" target="seqfeatures" expand="false">\r
+ <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>\r
+ <tocitem text="Sequence Features File" target="features.fileformat"/>\r
+ <tocitem text="User Defined Sequence Features" target="search"/>\r
+ <tocitem text="DAS Features Settings" target="das.viewing"/>\r
+ </tocitem>\r
+ <tocitem text="Web Services" target="webservice" expand="false">\r
+ <tocitem text="Sequence Alignment" target="msaservice" expand="false">\r
+ <tocitem text="Clustal Alignment" target="clustal"/>\r
+ <tocitem text="Muscle Alignment" target="muscle"/>\r
+ <tocitem text="MAFFT Alignment" target="mafft"/>\r
+ </tocitem>\r
+ <tocitem text="Secondary Structure Prediction" target="jnet"/>\r
+ </tocitem>\r
+ <tocitem text="Colour Schemes" target="colours" expand="false">\r
+ <tocitem text="ClustalX" target="colours.clustal"/>\r