X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fredundancy.html;h=350be1c5fa00bad5f072d725ef2719a04c22a516;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=e97e3b0aca6fc962471f730bc664fa1b5ef17789;hpb=e143a4bd499db90ed40cec0ac3626efb5937983b;p=jalview.git diff --git a/help/html/calculations/redundancy.html b/help/html/calculations/redundancy.html index e97e3b0..350be1c 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.
+