TreeFlow: Probabilistic modelling and automatic differentiation for phylogenetics

Probabilistic programming frameworks are powerful tools for statistical
modelling and inference. They are not immediately generalisable to
phylogenetic problems due to the particular computational properties of
the phylogenetic tree object. TreeFlow is a software library for
probabilistic programming and automatic differentiation with phylogenetic
trees. It implements inference algorithms for phylogenetic tree times and
model parameters, given a tree topology. We demonstrate how TreeFlow can
be used to quickly implement and assess new models. We also show that it
provides reasonable performance for gradient-based inference algorithms
compared to specialized computational libraries for phylogenetics.