[Jalview-discuss] Redundancy remova

[Jim Procter]

Hi Doran. Sorry for the late reply ...
On 05/03/2012 11:52, doranhen at post.tau.ac.il wrote:
> 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?
What is happening is that Jalview uses the alignment to calculate 
percentage identity between the sequences. This means that if there are 
no mutations, all the sequences are considered identical. If you want to 
remove redundant sequences from a set, then you should first use the 
'Remove all gaps' function, and then try the redundancy filter again.

I lodged a feature request about this last year, but haven't managed to 
get around to implementing it yet: http://issues.jalview.org/browse/JAL-743

Jim.