1 <?xml version="1.0" encoding="ISO-8859-1" ?>
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2 <!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">
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4 <tocitem text="Jalview Documentation" target="home" expand="true" >
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5 <tocitem text="What's new" target="new" expand="false">
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6 <tocitem text="EBI Sequence Fetcher" target="seqfetch"/>
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7 <tocitem text="New Output Format Controls" target="preferences"/>
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8 <tocitem text="Enhanced PDB Viewer" target="viewingpdbs"/>
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9 <tocitem text="Sequence Feature Styles" target="seqfeatures"/>
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11 <tocitem text="Release History" target="release"/>
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12 <tocitem text="Alignment Annotations" target ="alannotation" expand="false">
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13 <tocitem text="Conservation" target="calcs.alconserv"/>
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14 <tocitem text="Quality" target="calcs.alquality"/>
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16 <tocitem text="Input / Output" target="io"/>
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17 <tocitem text="Key Strokes" target="keys"/>
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18 <tocitem text="Making figures" target="export"/>
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19 <tocitem text="Editing Alignments" target ="edit"/>
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20 <tocitem text="Web Services" target="webservice" expand="false">
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21 <tocitem text="Clustal Alignment" target="clustal"/>
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22 <tocitem text="Muscle Alignment" target="muscle"/>
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23 <tocitem text="JNet Prediction" target="jnet"/>
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25 <tocitem text="Colour Schemes" target="colours" expand="false">
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26 <tocitem text="ClustalX" target="colours.clustal"/>
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27 <tocitem text="Zappo" target="colours.zappo"/>
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28 <tocitem text="Taylor" target="colours.taylor"/>
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29 <tocitem text="Hydrophobicity" target="colours.hydro"/>
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30 <tocitem text="Helix propensity" target="colours.helix"/>
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31 <tocitem text="Strand propensity" target="colours.strand"/>
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32 <tocitem text="Turn propensity" target="colours.turn"/>
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33 <tocitem text="Buried index" target="colours.buried"/>
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34 <tocitem text="Nucleotide colours" target="colours.nucleotide"/>
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35 <tocitem text="Blosum62" target="colours.blosum"/>
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36 <tocitem text="by Percentage Identity" target="colours.pid"/>
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37 <tocitem text="User Defined" target="colours.user"/>
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38 <tocitem text="Above Percentage Identity" target="colours.abovepid"/>
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39 <tocitem text="By conservation" target="colours.conservation"/>
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41 <tocitem text="Calculations" target="calculations" expand="false">
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42 <tocitem text="Sorting alignments" target="sorting"/>
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43 <tocitem text="Calculating trees" target="trees"/>
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44 <tocitem text="Principal Component Analysis" target="pca"/>
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45 <tocitem text="Pairwise Alignments" target="pairwise"/>
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46 <tocitem text="Remove Redundancy" target="redundancy"/>
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48 <tocitem text="Window Menus" target="menus" expand="false">
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49 <tocitem text="Desktop Window" target="desktopMenu"/>
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50 <tocitem text="Alignment Window" target="alMenu">
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51 <tocitem text="File Menu" target="alwFile"/>
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52 <tocitem text="Edit Menu" target="alwEdit"/>
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53 <tocitem text="View Menu" target="alwView"/>
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54 <tocitem text="Colour Menu" target="alwColour"/>
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55 <tocitem text="Calculation Menu" target="alwCalc"/>
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56 <tocitem text="Web Service Menu" target="wsMenu"/>
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57 <tocitem text="Annotation Menus" target="annotMenus"/>
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58 <tocitem text="Popup Menu" target="popMenu"/>
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61 <tocitem text="Memory Settings" target="memory" expand="false">
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62 <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>
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65 <tocitem text="Useful information" expand="true">
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66 <tocitem text="Amino Acid Table" target="aminoAcids"/>
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67 <tocitem text="Amino Acid Properties" target="aaProperties"/>
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68 <tocitem text="The Genetic Code" target="geneticCode"/>
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