1 <?xml version="1.0" encoding="ISO-8859-1" ?>
2 <!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">
4 <tocitem text="Jalview Documentation" target="home" expand="true" >
5 <tocitem text="What's new" target="new" expand="true">
6 <tocitem text="Release History" target="release"/>
7 <tocitem text="PDB Viewing with Jmol" target="pdbjmol"/>
8 <tocitem text="Mapping between Sequences" target="seqmappings"/>
10 <tocitem text="Editing Alignments" target ="edit"/>
11 <tocitem text="Cursor Mode" target="cursor"/>
12 <tocitem text="Key Strokes" target="keys"/>
13 <tocitem text="Input / Output" target="io"/>
14 <tocitem text="Making figures" target="export"/>
15 <tocitem text="Hidden Regions" target="hiddenRegions"/>
16 <tocitem text="Multiple Views" target="multipleviews"/>
17 <tocitem text="Sequence Features" target="seqfeatures" expand="false">
18 <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
19 <tocitem text="Sequence Features File" target="features.fileformat"/>
20 <tocitem text="User Defined Sequence Features" target="seqfeatcreat"/>
21 <tocitem text="Editing Sequence Features" target="seqfeatedit"/>
22 <tocitem text="DAS Feature Retrieval" target="das.viewing"/>
23 <tocitem text="DAS Feature Settings" target="das.settings"/>
25 <tocitem text="Web Services" target="webservice" expand="false">
26 <tocitem text="Sequence Alignment" target="msaservice" expand="false">
27 <tocitem text="Clustal Alignment" target="clustal"/>
28 <tocitem text="Muscle Alignment" target="muscle"/>
29 <tocitem text="MAFFT Alignment" target="mafft"/>
30 <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
32 <tocitem text="Secondary Structure Prediction" target="jnet"/>
34 <tocitem text="Colour Schemes" target="colours" expand="false">
35 <tocitem text="Background Dependent Text Colour" target="backdeptextcol"/>
36 <tocitem text="ClustalX" target="colours.clustal"/>
37 <tocitem text="Zappo" target="colours.zappo"/>
38 <tocitem text="Taylor" target="colours.taylor"/>
39 <tocitem text="Hydrophobicity" target="colours.hydro"/>
40 <tocitem text="Helix propensity" target="colours.helix"/>
41 <tocitem text="Strand propensity" target="colours.strand"/>
42 <tocitem text="Turn propensity" target="colours.turn"/>
43 <tocitem text="Buried index" target="colours.buried"/>
44 <tocitem text="Nucleotide colours" target="colours.nucleotide"/>
45 <tocitem text="Blosum62" target="colours.blosum"/>
46 <tocitem text="by Percentage Identity" target="colours.pid"/>
47 <tocitem text="User Defined" target="colours.user"/>
48 <tocitem text="Above Percentage Identity" target="colours.abovepid"/>
49 <tocitem text="By conservation" target="colours.conservation"/>
50 <tocitem text="By Annotation" target="colours.annotation"/>
52 <tocitem text="Calculations" target="calculations" expand="false">
53 <tocitem text="Sorting alignments" target="sorting"/>
54 <tocitem text="Calculating trees" target="trees"/>
55 <tocitem text="Principal Component Analysis" target="pca"/>
56 <tocitem text="Tree/PCA Input Data" target="recoverInputdata"/>
57 <tocitem text="Pairwise Alignments" target="pairwise"/>
58 <tocitem text="Remove Redundancy" target="redundancy"/>
60 <tocitem text="Alignment Annotations" target ="alannotation" expand="false">
61 <tocitem text="Conservation" target="calcs.alconserv"/>
62 <tocitem text="Quality" target="calcs.alquality"/>
63 <tocitem text="Consensus" target="calcs.consensus"/>
64 <tocitem text="Annotations File Format" target="annotations.fileformat"/>
66 <tocitem text="Viewing PDB Files" target="viewingpdbs" expand="false">
67 <tocitem text="Jmol Viewer" target="pdbjmol"/>
68 <tocitem text="Simple PDB Viewer" target="pdbmcviewer"/>
70 <tocitem text="Window Menus" target="menus" expand="false">
71 <tocitem text="Desktop Window" target="desktopMenu"/>
72 <tocitem text="Alignment Window" target="alMenu">
73 <tocitem text="File Menu" target="alwFile"/>
74 <tocitem text="Edit Menu" target="alwEdit"/>
75 <tocitem text="Select Menu" target="alwSelect"/>
76 <tocitem text="View Menu" target="alwView"/>
77 <tocitem text="Format Menu" target="alwFormat"/>
78 <tocitem text="Colour Menu" target="alwColour"/>
79 <tocitem text="Calculation Menu" target="alwCalc"/>
80 <tocitem text="Web Service Menu" target="wsMenu"/>
81 <tocitem text="Annotation Menus" target="annotMenus"/>
82 <tocitem text="Popup Menu" target="popMenu"/>
85 <tocitem text="Preferences" target="preferences"/>
86 <tocitem text="Memory Settings" target="memory" expand="false">
87 <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>
89 <tocitem text="Command Line" target="commandline" expand="false">
90 <tocitem text="Command Line Arguments" target="clarguments"/>
93 <tocitem text="Useful information" expa nd="true">
94 <tocitem text="Amino Acid Table" target="aminoAcids"/>
95 <tocitem text="Amino Acid Properties" target="aaProperties"/>
96 <tocitem text="The Genetic Code" target="geneticCode"/>