[Jalview-discuss] "Show values in textbox" for consensus in Jalview 2.5

[hari jayaram]

Hi I have a saved alignement generated from the clustalw service at EMBL-EBI.
When I launch Jalview from the clustalw site - I click on the
consensus and be presented with a "Show values in textbox" option
which then prints to a textbox the following information ( see below).
The second line of this information which indicates the consensus
sequence and the percentage conservation at that point.

This feature is however not available in jalview 2.5 . How can I open
any saved alignment in jalview 2.5 and obtain the  consensus
percentage for each position in the alignment for use in another
downstream analysis program.

Thanks
Hari


Show values in textbox" option output:


0.0, 0.0, 0.0, 0.0, 5.4054055, 0.0, 0.0, 5.4054055, 0.0, 0.0, 0.0,
5.4054055, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 18.918919, 21.621622, 18.918919, 18.918919, 21.621622, 16.216217,
18.918919, 21.621622, 21.621622, 29.72973, 13.513514, 16.216217,
27.027027, 5.4054055, 13.513514, 8.1081085, 10.810811, 13.513514,
16.216217, 24.324324, 48.648647, 13.513514, 0.0, 0.0, 13.513514,
27.027027, 37.837837, 24.324324, 16.216217, 16.216217, 21.621622,
18.918919, 45.945946, 37.837837, 72.97298, 32.432434, 13.513514,
18.918919, 48.648647, 24.324324, 27.027027, 89.189186, 5.4054055, 0.0,
0.0, 0.0, 0.0, 0.0, 35.135136, 40.54054, 62.162163, 29.72973,
37.837837, 78.37838, 21.621622, 18.918919, 35.135136, 45.945946,
24.324324, 0.0, 0.0, 0.0, 24.324324, 16.216217, 32.432434, 83.78378,
16.216217, 24.324324, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 21.621622, 18.918919, 29.72973, 45.945946, 18.918919,
24.324324, 72.97298, 21.621622, 18.918919, 45.945946, 29.72973,
24.324324, 13.513514, 91.89189, 51.351353, 18.918919, 16.216217, 0.0,
54.054054, 59.45946, 29.72973, 18.918919, 5.4054055, 29.72973,
40.54054, 16.216217, 16.216217, 32.432434, 21.621622, 21.621622,
54.054054, 16.216217, 16.216217, 0.0, 0.0, 5.4054055, 5.4054055, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
- 0%, - 0%, - 0%, - 0%, M 5%, - 0%, - 0%, I 5%, - 0%, - 0%, - 0%, K
5%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%,
- 0%, - 0%, C 18%, L 21%, E 18%, [IV] 18%, [IL] 21%, [KR] 16%, K 18%,
L 21%, K 21%, E 29%, [KN] 13%, D 16%, G 27%, [GS] 5%, R 13%, [RT] 8%,
I 10%, [AS] 13%, K 16%, I 24%, F 48%, [ELP] 13%, - 0%, - 0%, E 13%, L
27%, P 37%, D 24%, R 16%, E 16%, E 21%, V 18%, P 45%, D 37%, Y 72%, Y
32%, K 13%, I 18%, I 48%, K 24%, K 27%, P 89%, G 5%, - 0%, - 0%, - 0%,
- 0%, - 0%, M 35%, D 40%, L 62%, S 29%, T 37%, I 78%, E 21%, Q 18%, K
35%, L 45%, E 24%, - 0%, - 0%, - 0%, S 24%, K 16%, K 32%, Y 83%, K
16%, S 24%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, -
0%, - 0%, - 0%, L 21%, A 18%, E 29%, F 45%, E 18%, A 24%, D 72%, [IV]
21%, E 18%, L 45%, [IM] 29%, F 24%, K 13%, N 91%, A 51%, I 18%, R 16%,
- 0%, Y 54%, N 59%, G 29%, K 18%, R 5%, G 29%, S 40%, E 16%, L 16%, Y
32%, K 21%, D 21%, A 54%, [IL] 16%, E 16%, - 0%, - 0%, K 5%, V 5%, -
0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%,