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.
+