Code and Software

I develop and maintain computational tools for phylogenetics, genome annotation, metagenomics, network analysis, and computational infrastructure.

naive ATLAS

Metagenomic workflow for the recovery and analysis of microbial genomes across prokaryotes, microbial eukaryotes, viruses, and plasmids. Workflow includes quality control, assembly, binning, gene prediction, annotation, and quantification.

Project documentation / source

PhySortR

Creator and maintainer of an R package for screening and sorting phylogenetic trees, including exclusive and non-exclusive clade detection in traditional and extended Newick formats. CRAN version 1.0.9; DOI: 10.32614/CRAN.package.PhySortR.

Project documentation / source

Dinoflagellate Annotation Workflow

Workflow for protein-coding gene prediction in dinoflagellate genomes, integrating transcriptomic, proteomic, and ab initio evidence and accommodating non-standard splice-site biology.

Project documentation / source

Network Analysis Scripts

Python graph-tool utilities for graph construction, connected-component extraction, vertex annotation, graph layout, and visualization.

Project documentation / source

MAGS-CodeDev

Multi-agent graph-based software-development system that coordinates code generation, testing, diagnosis, review, and iteration across dependency-ordered modules in isolated worktrees and containers.

Project documentation / source

AgentBox

Rootless Podman-based, project-scoped sandbox for running coding agents with explicit filesystem and network permissions.

Project documentation / source