PhyloJunction: a computational framework for simulating, developing, and teaching evolutionary models

We introduce PhyloJunction, a computational framework designed to facilitate the prototyping, testing, and characterization of evolutionary models. PhyloJunction is distributed as an open-source Python library that can be used to implement a variety of models, through its flexible graphical modeling architecture and dedicated model specification language. Model design and use are exposed to users via command-line and graphical interfaces, which integrate the steps of simulating, summarizing, and visualizing data. This paper describes the features of PhyloJunction – which include, but are not limited to, a general implementation of a popular family of phylogenetic diversification models – and, moving forward, how it may be expanded to not only include new models, but to also become a platform for conducting and teaching statistical learning., , , # PhyloJunction: a computational framework for simulating, developing, and teaching evolutionary models [https://doi.org/10.5061/dryad.kkwh70sbq](https://doi.org/10.5061/dryad.kkwh70sbq) ## Supplementary files 1. A .pdf file (mendes_landis_24_supp.pdf - Zenodo) detailing the methods and results from analyses carried out to validate PhyloJunction; 2. A tarball (phylojunction_supp.tar.gz) with documentation (NOTES.md) and scripts necessary to reproduce the results presented in (1) above. ## Code/Software Documentation on how to install and use PhyloJunction can be found at [https://phylojunction.org](https://phylojunction.org). PhyloJunction's source code can be found on GitHub at [https://github.com/fkmendes/PhyloJunction/tree/main](https://github.com/fkmendes/PhyloJunction/tree/main).