Dodonaphy - a Software using Hyperbolic Space for Bayesian Phylogenetic Inference
Macaulay, Matthew; Darling, Aaron; Fourment, Mathieu (2022), Dodonaphy - a Software using Hyperbolic Space for Bayesian Phylogenetic Inference, Dryad, Dataset, https://doi.org/10.5061/dryad.6hdr7sr3p
Bayesian inference for phylogenetics is a gold standard for computing distributions of phylogenies. It faces the challenging problem of moving throughout the high-dimensional space of trees. However, hyperbolic space offers a low dimensional representation of tree-like data. In this paper, we embed genomic sequences into hyperbolic space and perform hyperbolic Markov Chain Monte Carlo for Bayesian inference. The posterior probability is computed by decoding a neighbour joining tree from proposed embedding locations. We empirically demonstrate the fidelity of this method on eight data sets. The sampled posterior distribution recovers the splits and branch lengths to a high degree. We investigated the effects of curvature and embedding dimension on the Markov Chain's performance. Finally, we discuss the prospects for adapting this method to navigate tree space with gradients.
This software embeds phylogenetic taxa in hyerbolic space to perform Bayesian inference. Version 1.0.0 includes a Markov Chain Monte Carlo (MCMC) that we compared to the state-of-art on eight datasets (previously published elsewhere). This package is implemented in Python3.9 with a simle command line interface provided.
Australian Research Council