Software
Below is a list of software I have developed, written in **Python**, with links to the code repositories and related publications.
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.
This package implements the Squirrel algorithm for reconstructing semi-directed phylogenetic level-1 networks from either four‐leaf quarnet sets or sequence alignments. :contentReference[oaicite:0]{index=0}
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. :contentReference[oaicite:1]{index=1}
An implementation of algorithms and heuristics for computing the scanwidth parameter of directed acyclic graphs (DAGs).
The repository contains the main algorithmic Python modules (including `scanwidth.py`, network extensions and heuristics), synthetic network generators, experiment management infrastructure, and plotting modules for analysing performance. :contentReference[oaicite:2]{index=2}
You can also browse all my code projects here:
https://github.com/nholtgrefe