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bioRxiv · 10.1101/2023.12.15.571907

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

Mendes, F. K.·Landis, M. J.
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Abstract

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.

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Mendes, F. K., Landis, M. J.. 2023-12-16. PhyloJunction: a computational framework for simulating, developing, and teaching evolutionary models. https://doi.org/10.1101/2023.12.15.571907

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