needle: Strictly global alignment?

[Guy Bottu]

> From owner-emboss at hgmp.mrc.ac.uk Fri Jun 13 18:00:04 2003
> X-Original-To: emboss at embnet.org
> Date: Fri, 13 Jun 2003 16:58:52 +0100
> From: Peter Rice <pmr at ebi.ac.uk>
> User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.0.2) 
Gecko/20030208 Netscape/7.02

> ... Though we could add terminal gaps as an option for those rare cases 
> where it could be useful. I note that stretcher also does not score 
> terminal gaps.

I did some testing and, if I am not wrong, stretcher DOES penalize terminal 
gaps.

For the rest, I agree with Jan Kim that needle and stretcher should allow the 
choice between penalizing and not penalizing terminal gaps and that the 
documentation should be more clear about this.

	Guy Bottu,
	BEN