3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
4 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 <title>T-COFFEE Annotation Scores</title>
23 <p><strong>Loading and viewing T-COFFEE Annotation Scores</strong></p>
24 <p>T-COFFEE score files like the <a href="#tcoffeeeg">one below</a> can be displayed on the alignment using the <strong><em>Colours→T-COFFEE Scores</em></strong>
25 or <strong><em>Colour → <a href="../colourSchemes/annotationColouring.html">Colour by Annotation</a></em></strong> options.</p>
26 <img src="../colourSchemes/colbytcoffee.png"/>
27 <p><strong><a name="tcoffeeeg">Example T-COFFEE Score file</a></strong><br/>
28 T-COFFEE score files like the one below can be dropped directly onto the corresponding alignment to visualize alignment confidence scores.
31 T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)
48 1PHT 999999999999999999999999998762112222543211112134
49 1BB9 99999999999999999999999999987-------4322----2234
50 1UHC 99999999999999999999999999987-------5321----2246
51 1YCS 99999999999999999999999999986-------4321----1-35
52 1OOT 999999999999999999999999999861-------3------1135
53 1ABO 99999999999999999999999999986-------422-------34
54 1FYN 99999999999999999999999999985-------32--------35
55 1QCF 99999999999999999999999999974-------2---------24
56 cons 999999999999999999999999999851000110321100001134
59 1PHT ----------5666642367889999999999889
60 1BB9 1111111111676653-355679999999999889
61 1UHC ----------788774--66789999999999889
62 1YCS ----------78777--356789999999999889
63 1OOT ----------78877--356789999999997-67
64 1ABO ----------687774--56779999999999889
65 1FYN ----------6888842356789999999999889
66 1QCF ----------6878742356789999999999889
67 cons 00100000006877641356789999999999889