Work

PhyloJunction: A Computational Framework for Simulating, Developing, and Teaching Evolutionary Models

Year: 2024

Type: article

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, thanks to 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 article 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.

Source: Systematic Biology

DOI: 10.1093/sysbio/syae048

Authors: Fábio K Mendes, Michael J Landis

Institutions: Louisiana State University, Washington University in St. Louis

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: National Science Foundation, National Institutes of Health, National Institute of Food and Agriculture, Fogarty International Center

Awards: G1932219530, Collaborative Research: Modeling the Origin and Evolution of Hawaiian Plants, G9000086082