help/help/html/io/tcoffeescores.html

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  22 <head>
  23 <title>T-COFFEE Annotation Scores</title>
  24 </head>
  25 <body>
  26   <p>
  27     <strong>Loading and viewing T-COFFEE Annotation Scores</strong>
  28   </p>
  29   <p>
  30     T-COFFEE score files like the <a href="#tcoffeeeg">one below</a> can
  31     be displayed on the alignment using the <strong><em>Colours&rarr;T-COFFEE
  32         Scores</em></strong> or <strong><em>Colour &rarr; <a
  33         href="../colourSchemes/annotationColouring.html">Colour
  34           by Annotation</a></em></strong> options.
  35   </p>
  36   <img src="../colourSchemes/colbytcoffee.png" />
  37   <p>
  38     <strong><a name="tcoffeeeg">Example T-COFFEE Score file</a></strong><br />
  39     T-COFFEE score files like the one below can be dropped directly onto
  40     the corresponding alignment to visualize alignment confidence
  41     scores.
  42   </p>
  43   <pre>
  44 T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)
  45 Cedric Notredame
  46 CPU TIME:0 sec.
  47 SCORE=90
  48 *
  49  BAD AVG GOOD
  50 *
  51 1PHT   :  89
  52 1BB9   :  90
  53 1UHC   :  94
  54 1YCS   :  94
  55 1OOT   :  93
  56 1ABO   :  94
  57 1FYN   :  94
  58 1QCF   :  94
  59 cons   :  90
  60
  61 1PHT   999999999999999999999999998762112222543211112134
  62 1BB9   99999999999999999999999999987-------4322----2234
  63 1UHC   99999999999999999999999999987-------5321----2246
  64 1YCS   99999999999999999999999999986-------4321----1-35
  65 1OOT   999999999999999999999999999861-------3------1135
  66 1ABO   99999999999999999999999999986-------422-------34
  67 1FYN   99999999999999999999999999985-------32--------35
  68 1QCF   99999999999999999999999999974-------2---------24
  69 cons   999999999999999999999999999851000110321100001134
  70
  71
  72 1PHT   ----------5666642367889999999999889
  73 1BB9   1111111111676653-355679999999999889
  74 1UHC   ----------788774--66789999999999889
  75 1YCS   ----------78777--356789999999999889
  76 1OOT   ----------78877--356789999999997-67
  77 1ABO   ----------687774--56779999999999889
  78 1FYN   ----------6888842356789999999999889
  79 1QCF   ----------6878742356789999999999889
  80 cons   00100000006877641356789999999999889
  81 </pre>
  82 <table border="1">
  83 <tr><th>Score</th><th>0</th><th>1</th><th>2</th><th>3</th><th>4</th><th>5</th><th>6</th><th>7</th><th>8</th><th>9</th></tr>
  84 <tr>
  85 <td>RGB colour</td>
  86 <td bgcolor="#6666FF">102, 102, 255</td>
  87 <td bgcolor="#00FF00">0, 255, 0</td>
  88 <td bgcolor="#66FF00">102, 255, 0</td>
  89 <td bgcolor="#CCFF00">204, 255, 0</td>
  90 <td bgcolor="#FFFF00">255, 255, 0</td>
  91 <td bgcolor="#FFCC00">255, 204, 0</td>
  92 <td bgcolor="#FF9900">255, 153, 0</td>
  93 <td bgcolor="#FF6600">255, 102, 0</td>
  94 <td bgcolor="#FF3300">255, 51, 0</td>
  95 <td bgcolor="#FF2000">255, 34, 0</td></tr>
  96 </table>
  97 </body>
  98 </html>