From: jprocter Date: Thu, 6 Sep 2012 22:02:56 +0000 (+0100) Subject: JAL-1065 documentation and image X-Git-Tag: Jalview_2_9~310 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=912d1f18a4915deee8a84d87383c602de0c7076f;p=jalview.git JAL-1065 documentation and image --- diff --git a/help/html/colourSchemes/colbytcoffee.png b/help/html/colourSchemes/colbytcoffee.png new file mode 100644 index 0000000..7e84e33 Binary files /dev/null and b/help/html/colourSchemes/colbytcoffee.png differ diff --git a/help/html/io/tcoffeescores.html b/help/html/io/tcoffeescores.html new file mode 100644 index 0000000..4d0d247 --- /dev/null +++ b/help/html/io/tcoffeescores.html @@ -0,0 +1,71 @@ + + + +T-COFFEE Annotation Scores + + +

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
+
+ + + \ No newline at end of file