[Bioperl-l] ClustalW Score?

[Kevin Brown]

> you're right --- it is not really my code, I was just 
> elaborating Kevin's example --- it would probably need to be 
> more specific or perhaps the last Score seen is sufficient 
> for what one is trying to capture?

I took that code from a pairwise clustal alignment script that I wrote
to deal with aligning a bunch of short sequences against a long one to
see where they line up at.  When all of them were fed to Clustal the
short sequences all ended up aligned to each other and not well aligned
to the longer sequence.  I only saw one score in the output from the
pairwise, so that is what I used to find a reasonable value.