needle: Strictly global alignment?

[Peter Rice]

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