Algebraic invariants for inferring 4-leaf semi-directed phylogenetic networks

A core goal of phylogenomics is to determine the evolutionary history of a set of species from biological sequence data. Phylogenetic networks are able to describe more complex evolutionary phenomena than phylogenetic trees, but are more difficult to accurately reconstruct. Recently, there has been growing interest in developing methods to infer semi-directed phylogenetic networks. As computing such networks can be computationally intensive, one approach to building such networks is to puzzle together smaller networks. Thus, it is essential to have robust methods for inferring semi-directed phylogenetic networks on small numbers of taxa. In this paper, we investigate an algebraic method for performing phylogenetic network inference from nucleotide sequence data on 4-leaf semi-directed phylogenetic networks by analysing the distribution of leaf-pattern probabilities. On simulated data, we found that we can correctly identify with high accuracy the undirected phylogenetic network for sequ..., , # Algebraic invariants for inferring 4-leaf semi-directed phylogenetic networks

Dataset DOI: [10.5061/dryad.44j0zpcrk](10.5061/dryad.44j0zpcrk)

## Description of the data and file structure

Simulated data and results from \"Algebraic Invariants for Inferring 4-leaf Semi-Directed Phylogenetic Networks\". Simulation and analysis tools available at [https://github.com/SR-Martin/4cycle_invariants](https://github.com/SR-Martin/4cycle_invariants).

### Files and variables

#### File: JC_simulated_data.tar.gz

**Description:** JC simulated alignments generated by the script `simulateJC.py`.  Alignments are in phylip format and organised according to the dataset. E.g. the directory `network0123` contains the alignments generated under the sunlet (0,1,2,3) used in Section 3.1. The directory `tree_ratio` contains the alignments for which the tree ratio is varied in Section 3.2, where e.g. the directory `g_.35` contains those alignments for which the tree ratio was 0.35. Each alignment file is na...,