filter.seqs filters columns with 70% gap not 100

I’ve observed filter.seqs’ default behavior remove columns with more than 70% gap characters as opposed to “a ‘-’ in every sequence” as described in the wiki. I think the 70% cutoff isn’t necessarily a bad thing, but either the wiki should be updated to match the program’s current behavior or the program should be modified to match the wiki’s description.


I’m not seeing what you’re seeing in the code. Can you send me an example?

I apologize for the delay in responding. I have been buried under a combination of work and snow…

As near as I can tell, the “bug” arose when I tried to visualize before and after filterings using ClustalX for Windows32.
Unfortunately, ClustalX doesn’t understand leading dot characters and therefore introduced subtle shifts in the alignment :oops:

I apologize for any panic I might have caused (and for linking a tasteless comic to boot).
I’ll go try to help someone else out on the forums for my penance…


Ah, the joy of clustal. No problem and thanks for the update.