X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fcalculations%2Fredundancy.html;h=5b1badb3629a325744833a6934fb83e0cbb8e53e;hb=5160a2b12eaed0e6fb398ec3ff3805e1630b9b83;hp=e97e3b0aca6fc962471f730bc664fa1b5ef17789;hpb=e143a4bd499db90ed40cec0ac3626efb5937983b;p=jalview.git diff --git a/help/html/calculations/redundancy.html b/help/html/calculations/redundancy.html index e97e3b0..5b1badb 100755 --- a/help/html/calculations/redundancy.html +++ b/help/html/calculations/redundancy.html @@ -1,15 +1,40 @@ - -
Removing redundancy
-Selecting this option brings up a window asking you to select a threshold. - If the percentage identity between two sequences (based on the - current alignment) exceeds this value one of the - sequences (the shorter) is discarded. The redundancy calculation is done when - the Apply button is pressed, and the undo button recovers the - original set or any previously calculated subset. The detection of - redundant sequences involves a pairwise comparison of all the - sequences, so you may have to wait a few moments when applying this to - large sequence sets.
- - + + + ++ Removing redundancy +
+
+ Selecting the option in the Alignment window's Edit
+ menu or pressing 'CONTROL+D' brings up a dialog box
+ asking you to select a threshold. If the percentage identity between
+ the aligned positions of any two sequences in the visible alignment
+ exceeds this value, the shorter sequence is discarded.
Note:
+ The redundancy calculation is done when the dialog box is opened.
+ For large numbers of sequences this can take a long time as all
+ pairs have to be compared.
+