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

[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!!!