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Phylogenetic Reference

A library of phylogenetic models has been created as part of TreePPL. These models can be found under models/phylo.

Constant rate birth-death​

  • models/phylo/crbd

The version crbd_quick.tppl uses a technique called Jan's walk to not waste information at the end of the branch. A tree (data) is provided. To compile do

tpplc models/phylo/crbd/crbd_quick.tppl models/phylo/crbd/alcedinidae.mc -m smc-bpf out.mc && mi compile out.mc

Now you can use the executable out [number of particles] [number of sweeps] to estimate the marginal likelihood of the model and get samples from the posterior of the lineage-splitting rate λ. Here, it is very crucial that you use an advanced inference method such as SMC-BPF or SMC-APF as the default importance sampling will not result in a good sample.

Feel free to experiment with the model, change the input, the priors, or the output.

ClaDS​

  • models/phylo/clads

clads.tppl in the model directory is a simple version of ClaDS that returns the speciation rate λ; however, it does not return the branch-specific rates. Feel free to extend it.