Comments (2)
xavierdidelot
commented on July 20, 2024
Dear Corinna,
Indeed ClonalFrameML does not estimate R separately. If you want to do this, you will need to multiply the value of R/theta with an estimate of theta. You could use the Watterson estimator which is given by: theta=L*G/An where L is the sum of the branch lengths in the recombination-corrected tree, G is the length of the alignment and An is the sum of the 1/i for i ranging from 1 to n-1 with n being your number of genomes.
Best wishes,
Xavier
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cbreusing
commented on July 20, 2024
Dear Xavier,
Thank you so much for your advice. This has helped me a lot.
Corinna
… On 1. Aug 2022, at 04:43, Xavier Didelot ***@***.***> wrote:
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