A Nexus website for the University of Wisconsin Research Software Engineer community.

Episode Clustering in Phylogenetic Networks

Public evidence package for the Instats report on responsible AI use in PhD-level research and research training. A global capability framework for university research leadership across 38 top-tier…

Plotting of phylogenies in Julia using Makie.

tutorial on some JuliaPhylo packages, focusing on comparative methods along networks

A library for conlanging

Julia package for the analysis of trait evolution along a phylogeny, including phylogenetic networks.

A flexible model for estimating thermal tolerance and sensitivity

Short scripts for converting genetic data between formats.

PhyloZoo: a Python package for working with phylogenetic networks and related evolutionary datatypes

Module for analysing admixture graphs

package to summarize features of a phylogenetic network, or features shared across a set of phylogenetic networks

Simulate a multispecies coalescent forward in time and make a plot

Julia package providing FileIO-compatible loading of phylogenetic tree and network data from various formats into arbitrary types of graph container types.

All of the scripts and initial data used in the simulation study to evaluate SNaQ.jl version 1.1 as well as the empirical study of swordtails and platyfishes (Xiphophorus: Poeciliidae).

A REPL-based AI coding copilot for Julia — connect to Anthropic Claude, OpenAI, Ollama, or any compatible API

Code implementation for "Neural Neighbor Join for Accurate Molecular Phylogenetic Inference"

Files for inference of 4-leaf 4-cycle phylogenetic networks from aligned DNA sequence data

Squirrel: a Python package for reconstructing level-1 phylogenetic networks from sequence alignments or four-leaved networks

PaNDA: a Python package for computing and maximizing phylogenetic diversity in phylogenetic networks

Quartet subsampling for inferring phylogenetic networks via sparse learning