Loading and viewing T-COFFEE Annotation Scores

T-COFFEE score files like the one below can be displayed on the alignment using the Colours→T-COFFEE Scores or Colour → Colour by Annotation options.

Example T-COFFEE Score file
T-COFFEE score files like the one below can be dropped directly onto the corresponding alignment to visualize alignment confidence scores.

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