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Updated: Sep 13, 2026

A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
TreeFlow: Probabilistic Modelling and Automatic Differentiation for Phylogenetics
Christiaan Swanepoel1,2, Mathieu Fourment3, Xiang Ji4
1Centre for Computational Evolution, The University of Auckland, Auckland, New Zealand.
Abstract:
Probabilistic modelling frameworks are powerful tools for statistical modelling and inference. They are not immediately generalizable to phylogenetic problems due to the particular computational properties of the phylogenetic tree object. TreeFlow is a software library for probabilistic modelling and automatic differentiation with phylogenetic trees. It embeds phylogenetic trees in the TensorFlow Probability framework, and implements inference algorithms for phylogenetic models given a fixed 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.
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