help/helpTOC.html

   1 <html><head><title>Jalview - Help </title></head>
   2 <body bgcolor=#F1F1F1>
   3 <p><center><strong>Contents</strong></center></p>
   4
   5 <br><a href="html/index.html" target=bodyframe>Jalview Documentation</a>
   6 <br>&nbsp;&nbsp;&nbsp;<a href="html/whatsNew.html" target=bodyframe>What's new</a>
   7 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/features/featureschemes.html" target=bodyframe>Graduated Feature Colours</a>
   8 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/features/featuresettings.html" target=bodyframe>Sort by Features</a>
   9 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/webServices/index.html" target=bodyframe>Envision2 Service</a>
  10 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/releases.html" target=bodyframe>Release History</a>
  11 <br>&nbsp;&nbsp;&nbsp;<a href="html/editing/index.html" target=bodyframe>Editing Alignments</a>
  12 <br>&nbsp;&nbsp;&nbsp;<a href="html/features/cursorMode.html" target=bodyframe>Cursor Mode</a>
  13 <br>&nbsp;&nbsp;&nbsp;<a href="html/keys.html" target=bodyframe>Key Strokes</a>
  14 <br>&nbsp;&nbsp;&nbsp;<a href="html/io/index.html" target=bodyframe>Input / Output</a>
  15 <br>&nbsp;&nbsp;&nbsp;<a href="html/io/export.html" target=bodyframe>Making Figures</a>
  16 <br>&nbsp;&nbsp;&nbsp;<a href="html/features/hiddenRegions.html" target=bodyframe>Hidden Regions</a>
  17 <br>&nbsp;&nbsp;&nbsp;<a href="html/features/multipleViews.html" target=bodyframe>Multiple Views</a>
  18 <br>&nbsp;&nbsp;&nbsp;<a href="html/calculations/treeviewer.html" target=bodyframe>Viewing Trees</a>
  19 <br>&nbsp;&nbsp;&nbsp;<a href="html/features/seqfetch.html" target=bodyframe>Fetching Sequences</a>
  20 <br>&nbsp;&nbsp;&nbsp;<a href="html/features/seqfeatures.html" target=bodyframe>Sequence Features</a>
  21 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/features/featuresettings.html" target=bodyframe>Sequence Feature Settings</a>
  22 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/features/featuresFormat.html" target=bodyframe>Sequence Features File</a>
  23 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/features/featureschemes.html" target=bodyframe>Feature Colourschemes</a>
  24 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/features/creatinFeatures.html" target=bodyframe>User Defined Sequence Features</a>
  25 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/features/editingFeatures.html" target=bodyframe>Editing Sequence Features</a>
  26 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/features/dasfeatures.html" target=bodyframe>DAS Feature Retrieval</a>
  27 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/features/dassettings.html" target=bodyframe>DAS Feature Settings</a>
  28 <br>&nbsp;&nbsp;&nbsp;<a href="html/webServices/index.html" target=bodyframe>Web Services</a>
  29 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/webServices/msaclient.html" target=bodyframe>Sequence Alignment</a>
  30 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/webServices/clustalw.html" target=bodyframe>Clustal Alignment</a>
  31 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/webServices/muscle.html" target=bodyframe>Muscle Alignment</a>
  32 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/webServices/mafft.html" target=bodyframe>MAFFT Alignment</a>
  33 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/webServices/msaclient.html" target=bodyframe>Multiple Alignment Subjobs</a>
  34 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/webServices/jnet.html" target=bodyframe>Secondary Structure Prediction</a>
  35 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/features/seqfetch.html" target=bodyframe>Sequence Retrieval</a>
  36 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/webservices/dbreffetcher.html" target=bodyframe>Database Reference Retrieval</a>
  37 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/features/dasfeatures.html" target=bodyframe>DAS Feature Retrieval</a>
  38 <br>&nbsp;&nbsp;&nbsp;<a href="html/na/index.html" target=bodyframe>Nucleic Acid Support</a>
  39 <br>&nbsp;&nbsp;&nbsp;<a href="html/colourSchemes/index.html" target=bodyframe>Colour Schemes</a>
  40 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/colourSchemes/textcolour.html" target=bodyframe>Background Dependent Text Colour</a>
  41 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/colourSchemes/clustal.html" target=bodyframe>ClustalX</a>
  42 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/colourSchemes/zappo.html" target=bodyframe>Zappo</a>
  43 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/colourSchemes/taylor.html" target=bodyframe>Taylor</a>
  44 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/colourSchemes/hydrophobic.html" target=bodyframe>Hydrophobicity</a>
  45 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/colourSchemes/helix.html" target=bodyframe>Helix propensity</a>
  46 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/colourSchemes/strand.html" target=bodyframe>Strand propensity</a>
  47 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/colourSchemes/turn.html" target=bodyframe>Turn propensity</a>
  48 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/colourSchemes/buried.html" target=bodyframe>Buried index</a>
  49 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/colourSchemes/nucleotide.html" target=bodyframe>Nucleotide colours</a>
  50 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/colourSchemes/purinepyrimidine.html" target=bodyframe>Purine/Pyrimidine colours</a>
  51 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/colourSchemes/blosum.html" target=bodyframe>Blosum62</a>
  52 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/colourSchemes/pid.html" target=bodyframe>by Percentage Identity</a>
  53 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/colourSchemes/user.html" target=bodyframe>User Defined</a>
  54 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/colourSchemes/abovePID.html" target=bodyframe>Above Percentage Identity</a>
  55 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/colourSchemes/conservation.html" target=bodyframe>By conservation</a>
  56 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/colourSchemes/annotationColouring.html" target=bodyframe>By Annotation</a>
  57 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/colourSchemes/rnahelicesColouring.html" target=bodyframe>By RNA Helices</a>
  58 <br>&nbsp;&nbsp;&nbsp;Calculations
  59 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/calculations/sorting.html" target=bodyframe>Sorting alignments</a>
  60 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/calculations/tree.html" target=bodyframe>Calculating trees</a>
  61 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/calculations/pca.html" target=bodyframe>Principal Component Analysis</a>
  62 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/calculations/recoverInputdata.html" target=bodyframe>Tree/PCA Input Data</a>
  63 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/calculations/pairwise.html" target=bodyframe>Pairwise Alignments</a>
  64 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/calculations/redundancy.html" target=bodyframe>Remove Redundancy</a>
  65 <br>&nbsp;&nbsp;&nbsp;<a href="html/features/annotation.html" target=bodyframe>Alignment Annotations</a>
  66 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/calculations/conservation.html" target=bodyframe>Conservation</a>
  67 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/calculations/structureconservation.html" target=bodyframe>RNA Structure Conservation</a>
  68 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/calculations/quality.html" target=bodyframe>Quality</a>
  69 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/calculations/consensus.html" target=bodyframe>Consensus</a>
  70 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/features/annotationsFormat.html" target=bodyframe>Annotations File Format</a>
  71 <br>&nbsp;&nbsp;&nbsp;<a href="html/features/viewingpdbs.html" target=bodyframe>Viewing PDB Files</a>
  72 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/features/jmol.html" target=bodyframe>Jmol Viewer</a>
  73 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/features/pdbviewer.html" target=bodyframe>Simple PDB Viewer</a>
  74 <br>&nbsp;&nbsp;&nbsp;<a href="html/vamsas/index.html" target=bodyframe>VAMSAS Data Exchange</a>
  75 <br>&nbsp;&nbsp;&nbsp;<a href="html/menus/index.html" target=bodyframe>Window Menus</a>
  76 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/menus/desktopMenu.html" target=bodyframe>Desktop Window</a>
  77 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/menus/alignmentMenu.html" target=bodyframe>Alignment Window</a>
  78 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/menus/alwfile.html" target=bodyframe>File Menu</a>
  79 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/menus/alwedit.html" target=bodyframe>Edit Menu</a>
  80 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/menus/alwselect.html" target=bodyframe>Select Menu</a>
  81 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/menus/alwview.html" target=bodyframe>View Menu</a>
  82 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/menus/alwformat.html" target=bodyframe>Format Menu</a>
  83 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/menus/alwcolour.html" target=bodyframe>Colour Menu</a>
  84 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/menus/alwcalculate.html" target=bodyframe>Calculation Menu</a>
  85 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/menus/wsmenu.html" target=bodyframe>Web Service Menu</a>
  86 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/menus/alwannotations.html" target=bodyframe>Annotation Menus</a>
  87 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/menus/popupMenu.html" target=bodyframe>Popup Menu</a>
  88 <br>&nbsp;&nbsp;&nbsp;<a href="html/features/preferences.html" target=bodyframe>Preferences</a>
  89 <br>&nbsp;&nbsp;&nbsp;<a href="html/memory.html" target=bodyframe>Memory Settings</a>
  90 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/jalviewjnlp.html" target=bodyframe>JNLP with extra memory parameters</a>
  91 <br>&nbsp;&nbsp;&nbsp;<a href="html/features/commandline.html" target=bodyframe>Command Line</a>
  92 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/features/clarguments.html" target=bodyframe>Command Line Arguments</a>
  93 <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="html/features/groovy.html" target=bodyframe>Groovy Shell</a>
  94 <br>&nbsp;&nbsp;&nbsp;<a href="html/privacy.html" target=bodyframe>Privacy</a>
  95 <br>Useful information
  96 <br>&nbsp;&nbsp;&nbsp;<a href="html/misc/aminoAcids.html" target=bodyframe>Amino Acid Table</a>
  97 <br>&nbsp;&nbsp;&nbsp;<a href="html/misc/aaproperties.html" target=bodyframe>Amino Acid Properties</a>
  98 <br>&nbsp;&nbsp;&nbsp;<a href="html/misc/geneticCode.html" target=bodyframe>The Genetic Code</a>