Phyddle: software for phylogenetic model exploration with deep learning.

ABSTRACT: Many realistic phylogenetic models lack tractable likelihood functions, prohibiting their use with standard inference methods. We present phyddle, a pipeline-based toolkit for performing phylogenetic modeling tasks using likelihood-free deep learning approaches. phyddle coordinates modeling tasks through five analysis steps ( Simulate, Format, Train, Estimate , and Plot ) that transform raw phylogenetic datasets as input into numerical and visualized model-based output. Benchmarks show that phyddle accurately performs a range of inference tasks, 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. phyddle has a flexible command

SUBMITTER: Landis MJ 

PROVIDER: S-EPMC11326143 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature