Thanks so much for your rapid response.
- do you need GeneRax to estimate the per-species-branch DTL rates, or do you want to set them yourself?
I would love to let GeneRax to estimate the per-species-branch DTL rates. But for me, this sounds more like a "free-rate" model for every branch. I am wondering if I could constrain a group of branches with all of them having the same DTL rates but with another group having a different kind of rates? (For example, branches 1-10 have the same D=0.1, L=0.1, T=0.1, S=1 estimated by GeneRax and branches 11-20 also have the same rates but with D=0.5,L=0.5,T=0.1,S=1. And this is more like a "partially-free-rate" model which is helpful to test evolutionary hypotheses in comparative biology.)
- should I output the per-species-branch DTL rates in some file?
It will be very helpful! If it is available, please let me know. Thank you!
I think a "free-rate" model is good enough and I also noticed a "global-rate" model is alreday supported in GeneRax. I may ask for too much for a "partially-free-rate" model and it may take some time and effort to add this feature/function. So I guess I will just focus on the per-species-branch DTL rates first but eagerly look forward to a "partially-free-rate" model.
Really appreciate your help and I am again amazed that this tool is well maintained by you and your group.