I thought we addressed this on the BP list?

You can pass in a -QUIET flag to the TCoffee when you run it to supress printing to the screen as well. Read the whole module documentation at some point to get a sense of what all you can do.

The score field would need to be captured in the module which parses Bio::AlignIO::clustalw. As I believe I already wrote to you, you will need to modify the module to parse the SCORE out of the header. It is pretty simple and you can store the score in the Bio::SimpleAlign object that is created. You just need to modify the regexp where the CLUSTAL header is parsed and grab the SCORE out.