I'm only able to look at the paper in my spare time, and I had no spare time for the past few days. Also, quite frankly, I didn't know if your problem had been solved already or not.
Did the bioperl suggestions lead anywhere for you?
I'll resume reading the paper tomorrow. If you have any further reading material that might be helpful, please let me know. I can be reached more directly at firstname.lastname@example.org.
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