in reply to Re: Virus toy model
in thread Virus toy model^2

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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Re^3: Virus toy model
by biohisham (Priest) on Jun 30, 2011 at 01:33 UTC
    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

    David R. Gergen said "We know that second terms have historically been marred by hubris and by scandal." and I am a two y.o. monk today :D, June,12th, 2011...