Extracting Individual branch rates

[Perry Wood]

Hi everyone,

I am looking at comparing some speciation, extinction, and diversification, rates across a phylogenetic tree for some organisms from different historical backgrounds (continental origin, vs. insular origin, etc...).  I know that this can be done using the getCladeRates function in BAMMtools and I can specify the node(s) of interest, however not all of the groups are monophyletic and I wish to extract the rates for individual branches.

So my question is: can I use the edgelabels instead of the nodelabels to extract these rates for single branches using the getCladeRates? Or is there a better way to go about obtaining this information?

Any help or suggestions would be greatly appreciated,

Thanks,

Perry

[pasca...@gmail.com]

Hi Perry,

Yeah, getCladeRates() generally makes more sense for monophyletic groups, although you can exclude multiple nodes. But it will return a mean clade-wide rate for each posterior sample, not branch specific rates.

If you want branch specific rates, the function getMarginalBranchRateMatrix() will give you what you are probably looking for: mean rates per branch, and for each posterior sample.

-Pascal