Interpret and improve subsection 'The effect of mutation rate'

richelbilderbeek commented 4 years ago

Copy-paste from response letter:

The height of the tree in units of substitutions will be a factor: when the tree is small (<< 0.1 substitutions) sequences will have many constant sites, and the tree cannot be reliably recovered. When the tree is large (>>1 substitutions), there will be saturations and it will be impossible to recover the tree. In the example, a distance of 1 is used (tree height = 10, mutation rate = 0.1), but not explained why that is a good combination. Some discussion around this would be useful.

Definitely! We have added this, also as a worked example in the Appendix, section 'The effect of mutation rate'

[...]
[X] https://github.com/richelbilderbeek/pirouette_article/issues/59: Add worked examples with mutation rates from 0.0125, 0.025, 0.05, 0.1, 0.2, 0.4, 0.8, at https://github.com/richelbilderbeek/pirouette_example_24
[ ] https://github.com/richelbilderbeek/pirouette_article/issues/70: Describe, section 'The effect of mutation rate'

richelbilderbeek commented 4 years ago

I'll take this one :+1:

richelbilderbeek commented 4 years ago

I close this Issue. I use paper now instead :+1:

richelbilderbeek / pirouette_article

Interpret and improve subsection 'The effect of mutation rate' #70