I have had a number of queries from users on my system about what
appears (to them) to be major differences between the output from pileup
in GCG 8 and GCG 9.
This seems to be due to the new default scoring matrix; does anyone
know what the rationale was behind this change, and why does it
produce such different answers to the previous GCG version? This
seems to have confused a lot of users. Of course I can tell them to
use -matrix=oldpep.cmp if they want the same results as GCG 8, but how
should they determine which is the appropriate scoring matrix to use?