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.