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JAL-1065 documentation and image
authorjprocter <jprocter@compbio.dundee.ac.uk>
Thu, 6 Sep 2012 22:02:56 +0000 (23:02 +0100)
committerjprocter <jprocter@compbio.dundee.ac.uk>
Thu, 6 Sep 2012 22:02:56 +0000 (23:02 +0100)
help/html/colourSchemes/colbytcoffee.png [new file with mode: 0644] patch | blob
help/html/io/tcoffeescores.html [new file with mode: 0644] patch | blob

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+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+-->
+<head>
+<title>T-COFFEE Annotation Scores</title>
+</head>
+<body>
+<p><strong>Loading and viewing T-COFFEE Annotation Scores</strong></p>
+<p>T-COFFEE score files like the <a href="#tcoffeeeg">one below</a> can be displayed on the alignment using the <strong><em>Colours&rarr;T-COFFEE Scores</em></strong>
+or <strong><em>Colour &rarr; <a href="../colourSchemes/annotationColouring.html">Colour by Annotation</a></em></strong> options.</p>
+<img src="../colourSchemes/colbytcoffee.png"/>
+<p><strong><a name="tcoffeeeg">Example T-COFFEE Score file</a></strong><br/>
+T-COFFEE score files like the one below can be dropped directly onto the corresponding alignment to visualize alignment confidence scores.
+</p>
+<pre>
+T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)
+Cedric Notredame 
+CPU TIME:0 sec.
+SCORE=90
+*
+ BAD AVG GOOD
+*
+1PHT   :  89
+1BB9   :  90
+1UHC   :  94
+1YCS   :  94
+1OOT   :  93
+1ABO   :  94
+1FYN   :  94
+1QCF   :  94
+cons   :  90
+
+1PHT   999999999999999999999999998762112222543211112134
+1BB9   99999999999999999999999999987-------4322----2234
+1UHC   99999999999999999999999999987-------5321----2246
+1YCS   99999999999999999999999999986-------4321----1-35
+1OOT   999999999999999999999999999861-------3------1135
+1ABO   99999999999999999999999999986-------422-------34
+1FYN   99999999999999999999999999985-------32--------35
+1QCF   99999999999999999999999999974-------2---------24
+cons   999999999999999999999999999851000110321100001134
+
+
+1PHT   ----------5666642367889999999999889
+1BB9   1111111111676653-355679999999999889
+1UHC   ----------788774--66789999999999889
+1YCS   ----------78777--356789999999999889
+1OOT   ----------78877--356789999999997-67
+1ABO   ----------687774--56779999999999889
+1FYN   ----------6888842356789999999999889
+1QCF   ----------6878742356789999999999889
+cons   00100000006877641356789999999999889
+</pre>
+
+</body>
+</html>
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