phyddle: Software for Exploring Phylogenetic Models with Deep Learning

Phylogenies contain a wealth of information about the evolutionary history and process that gave rise to the diversity of life. This information can be extracted by fitting phylogenetic models to trees. However, many realistic phylogenetic models lack tractable likelihood functions, prohibiting their use with standard inference methods. We present phyddle, pipeline-based software for performing phylogenetic modeling tasks on trees using likelihood-free deep learning approaches. phyddle has a flexible command-line interface, making it easy to integrate deep learning approaches for phylogenetics into research workflows. phyddle coordinates modeling tasks through five pipeline analysis steps (Simulate, Format, Train, Estimate, and Plot) that transform raw phylogenetic data sets as input into numerical and visual model-based output. We conduct three experiments to compare the accuracy of likelihood-based inferences against deep learning-based inferences obtained through phyddle. Benchmarks show that phyddle accurately performs the inference tasks for which it was designed, such as estimating macroevolutionary parameters, selecting among continuous trait evolution models, and passing coverage tests for epidemiological models, even for models that lack tractable likelihoods. Learn more about phyddle at https://phyddle.org.