Software
Below is a list of software I have developed, written in Python, with links to the code repositories and related publications.
PhyloZoo is a Python package for working with phylogenetic networks and related evolutionary data types, designed as foundational infrastructure for phylogenetic network analysis in Python.
It provides validated directed and semi-directed network representations, support for quartets/splits/distance matrices and sequence alignments, flexible Matplotlib-based visualization, standard phylogenetic file formats, and performance-focused routines powered by NumPy (with optional Numba acceleration).
This package implements the Squirrel algorithm for reconstructing semi-directed phylogenetic level-1 networks from either four‐leaf quarnet sets or sequence alignments.
It provides both a graphical user interface (GUI) for non-programmers and a full Python API for advanced users, enabling simulation, inference and visualisation of reticulate evolutionary histories.
A Python package designed for exploration and maximization of phylogenetic diversity in phylogenetic networks.
It supports generation and handling of phylogenetic network instances, computes diversity‐based optimization criteria, and includes interactive visualizations and algorithmic pipelines for network‐level diversity analyses.
An implementation of algorithms and heuristics for computing the scanwidth parameter of directed acyclic graphs (DAGs).
You can also browse all my code projects here:
https://github.com/nholtgrefe