how to calculate the r/m value for subclade of a tree？

[Tonny-zhou]

Dear developer,

Thanks for this great tool to detect the recombination events in bacterial genome!

I have a question, i.e., a subclade of a tree consisted of eight strains，and if i want to obtain the r/m values of the subclade, should i calculate the mean r/m values of the eight strains, or just calculate the r/m value of the node of the most common ancestor of these eight strains. I'm new in the field of phylogeny, so could you please answer this question.

Yours, Tonny

[xavierdidelot]

Hi Tonny,

If you run with -embranch true you can compute r/m for each branch, and you could average across the branches of a clade to compute the r/m for a clade. A much simpler option would be to run ClonalFrameML on just the clade. I think eight strains should be enough for this to work well.

Best wishes, Xavier

[Tonny-zhou]

Sorry to bother you again. I'm a beginnger in the field of phylogeneti tree. Could you please tell me that for the following picture (a subclde of a tree), wthether the r/m value of branches X1-5 should be included to compute r/m value for this clade, or we only need to average the r/m values of branches A-G to compute the r/m value for this clade.

Sorry to bother you again and many thanks.

[xavierdidelot]

No worries, you should use all branches X1-X5 AND A-G. Actually you could consider excluding X5 since it is not really part of the subclade. But all other branches should definitely be used.

[Tonny-zhou]

Thank you very much!!!