Dear all,
When I work with MSAs that contain large gaps, I encounter the  
following problem when I try to remove redundancy: it tells me that  
all sequences except the top one are redundant (90%) although I know  
for a fact that they are not all redundant. Did any of you encounter  
this problem? if so, how do you fix it?

Thank you ,
Doran Hendin-Barak

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