I just now saw this script that you added. Your knowledge of biology tells me you work in a related field. Most of the parameters such as rate, and a mutation probability table I will be taking directly from wet lab/ primary literature findings. I have some good estimates in mind. I am aware of the many issues with modeling biological systems, but in this case I have several natural test sets. This toy model is to be used only to assess the effect of uneven and perhaps biased sequence sampling. I will go over this script you sent tonight it looks much better than the one I made haha.
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