needle: Strictly global alignment?

Peter Rice pmr at ebi.ac.uk
Mon Jun 16 09:22:32 UTC 2003


Guy Bottu wrote:
> I did some testing and, if I am not wrong, stretcher DOES penalize terminal 
> gaps.

Oops. This does seem to be true.

In that case, we do need to update the documentation, and provide the 
option to switch the terminal gap penalties on/off.

We may need to consider changing the default behaviour of one of the 
programs too.

Thanks for pointing it out.

Peter




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