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DOI: 10.4121/c679cd3c-0815-4021-a727-bcb8b9174b27

Julien, Esther; Bernardini, Giulia; Stougie, Leen; van Iersel, Leo (2023): Source code for the paper "Constructing Phylogenetic Networks via Cherry Picking and Machine Learning". Version 1. 4TU.ResearchData. software. https://doi.org/10.4121/c679cd3c-0815-4021-a727-bcb8b9174b27.v1

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Categories

• Applied Mathematics
• Evolutionary Biology
• Mathematical Sciences
• Biological Sciences

Keywords

Cherry Picking Heuristic Hybridization Machine Learning Phylogenetics

Licence

MIT

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by Esther Julien, Giulia Bernardini, Leen Stougie, Leo van Iersel

The contents of this repository is the source code for the paper "Constructing Phylogenetic Networks via Cherry Picking and Machine Learning" by Giulia Bernardini, Leo van Iersel, Esther Julien, and Leen Stougie. The research question for this project is the following: "Can machine learning increase the performance of a heuristic to construct phylogenetic networks given a set of phylogenetic trees with the same set of taxa?" This question has been answered by formalizing a method that uses ML and so-called method "cherry picking", and performing numerical experiments based on python code.

History

• 2023-03-30 first online, published, posted

Publisher

4TU.ResearchData

Format

.py files for code, .joblib for machine learning models, and text files for test instances (in newick format)

Organizations

TU Delft, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft Institute of Applied Mathematics