my script overlooked the mutation probability scores per base (unperlish laziness and lack of intuition at that moment) whereas yours has focused mainly on that, my approach was to provide room for the more common mutations rather than consulting with lesser common ones that may or may not be categorized as nonsense. While the user has a say at providing the number of replications to be conducted (a more prudent approach will have to consider that as the replication is repeated over and over there are more chances for errors to show, but my program and so is yours it seems were more obsessed with making mutations happen at the first level of replication and not based on the hierarchy that you indicated in your OP that each seq may generate more seq in a tree fashion)...

I find your incorporation of the mutation table so marvelous yet I have some comments on the implementation however that I'll share after running your program. Combining these two programs though is a worthwhile learning opportunity.

p.s. Yes, I work as a bioinformatician