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xavierdidelot / ClonalFrameML

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
GNU General Public License v3.0
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Calculate nucleotide diversity within and outside the clonal frame #108

Closed megaptera-helvetiae closed 4 years ago

megaptera-helvetiae commented 4 years ago

Dear Xavier, as you can see in issue #107, we are getting a bit more adventurous. Hence also my next question: Is there a way in ClonalFrameML to calculate nucleotide diversity within and outside the clonal frame (so including and excluding the parts that are recombining)? This would be similar to the output of Gubbins: https://sanger-pathogens.github.io/gubbins/

Thank you.

Laetitia and my allies.

xavierdidelot commented 4 years ago

I would say that the best way to do this is to compare the branch lengths in the tree before correcting for recombination (ie the tree input file of ClonalFrameML) and after correcting for recombination (ie the tree output file of ClonalFrameML). If by "diversity" you mean pairwise diversity, you could calculate and compare the patristic distance between pairs of leaves in both trees.