CLUSTERING PHYLOGENETIC TREES

This repository contains code for computing clustering of phylogenetic trees by interpreting the trees as points in the tropical torus $\mathbb{R}^n/\mathbb{R}\mathbf{1}$ and clustering them with respect to the tropical asymmetric distance (Comăneci, Joswig, 2024). The code builds upon Andrei Comăneci's implementation of this distance within Polymake and OSCAR.

The files in this repository are structured as follows:

• clustering.jl contains the essential function cluster for computing the clustering of phylogenetic trees.
• examples.jl shows how clustering a synthetic dataset of hundred trees on four taxa is performed. This case is sufficiently low dimensional to also be visualized.
• inexact.jl contains helper functions for working with data with floating point coefficients, in particular for working with numerical artifacts.
• apicomplexa-clustering.jl contains code for clustering the apicomplexa data set reported on in our paper.