How to mirror nodes that are not calibrated in MCMCTree

[Bruce Onisko]

Dear all,

I have a phylogeny with calibrated and cross braced nodes.

But there are other nodes in the tree which could be mirrored (if I knew how!) for which I do NOT have calibration data.

Does anyone know how to do this?

I calibrate my trees using Sandy's script Include_calibrations.R using a calibrations.csv file that includes the nodes (and duplicates) including calibration data.

Thanks!

Bruce

[Sandra AC]

Hi Bruce,

Thanks for your message! If you visit the PAML Wiki (section MCMCtree) and search for variable "duplication", you will see the following section at the end of the documentation:



You can see that the examples above have labels '#2' (i.e., in different formats, you can choose the one you prefer!) to indicate that the MRCA of A1, A2, and A3 is to be cross-braced with the MRCA of B1, B2, B3, thus the same posterior time density will be expected for this node age -- this is illustrated in the Figure you will find in the PAML Wiki, right below the information I pasted above:

Hope this answers your question!

All the best,
Sandy

[Bruce Onisko]

Thanks Sandy!  Problem solved.

BTW, to anyone interested here is the ReadMe showing  step-by-step methods to create calibrated trees:

https://github.com/sabifo4/LUCA-divtimes/blob/main/00_data_formatting/README.md

Bruce