zhaoxing-wu/phylodiamond.jl

Method to estimate phylogenetic networks from algebraic invariants

PhyloDiamond.jl

Overview

PhyloDiamond.jl is a Julia package for ultrafast learning of 4-node hybridization cycles in phylogenetic networks using algebraic invariants.

Input data:

• A concordance factor table, or
• A file containing gene trees

Usage

PhyloDiamond.jl is a Julia package, so the user needs to first install Julia, and then install the package.

To install Julia, follow the instructions in here.

To install the package, type inside Julia:

]
add PhyloDiamond

Help and errors

To get help, check the documentation here. Please report any bugs and errors by opening an issue.

Citation

If you use PhyloDiamond.jl in your work, we kindly ask that you cite the following paper:

@article{wu_solis-lemus_2022,
author = {Wu, Z. and Sol'{i}s-Lemus, C.},
year = {2022},
title = {{Ultrafast learning of 4-node hybridization cycles in phylogenetic networks using algebraic invariants}},
url={https://arxiv.org/abs/2211.16647v1}
}

License

PhyloDiamond.jl is licensed under a MIT License.

Contributions

Users interested in expanding functionalities in PhyloDiamond.jl are welcome to do so. See details on how to contribute in CONTRIBUTING.md.