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richelbilderbeek / razzo

Research project by Giovanni Laudanno and Richel J.C. Bilderbeek
GNU General Public License v3.0
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Check mutation rate #299

Closed richelbilderbeek closed 5 years ago

richelbilderbeek commented 5 years ago

While working on my thesis, I've found some evidence that the mutation rate is twice as high as I would have expected.

If the mutation rate indeed that much, it would explain some results that I dubbed 'the Achilles Heel':

20190909_are_results_results

Get the distribution of the fraction of mutations per mutation rate:

histograms

Using histograms on a facet grid, or using density plots in one grid would be equally fine.

richelbilderbeek commented 5 years ago

Here are the results:

issue_299

richelbilderbeek commented 5 years ago

Tree crown age is 1. The algorithm only counts the changed nucleotides.

richelbilderbeek commented 5 years ago

A wider range:

issue_299

richelbilderbeek commented 5 years ago

I feel a mutation rate of 0.5 / crown_age (as we do in razzo) is fine.

richelbilderbeek commented 5 years ago

I think I had a misconception when creating this Issue: everything works as expected.