Software
Open-source tools from the lab for phylogenetic clustering, pangenome graphs and nanopore sequencing of the virome. If you use one in published work, please cite the paper listed with it.
EPI-ClusT
Empirical Phylogeny Informed Cluster Tool
A distance-free way to define clusters in phylogenetic trees, built for inferring HIV transmission clusters from viral sequences.
GFA2Network
Memory-efficient GFA to graph converter
Streams pangenome variation graphs in GFA format into NetworkX, igraph or SciPy sparse matrices without loading the whole file, for graph-genome analyses of viruses.
AnelloFlow
Anellovirus discovery from nanopore reads
A pipeline that detects and characterizes anelloviruses in samples sequenced with our rolling-circle amplification and nanopore protocol.
Cite: Long-Read Nanopore-Based Sequencing of Anelloviruses Viruses 2024
ONT-RCA Error Profiler
Error rates for nanopore sequencing of circular genomes
Measures base-level error rates (substitutions, insertions, deletions and soft clips) in nanopore sequencing of RCA-amplified circular genomes, with depth simulation, virome backgrounds and circular reference handling.
Cite: Read-Level Error Characterization of Rolling-Circle Amplification-Based Nanopore Sequencing of the Circular DNA Virome Viruses 2026
Platforms
AI-powered platform for medical education
Learners work through clinical cases in dialogue with an AI tutor that asks Socratic questions and gives feedback against reasoning rubrics, and faculty build the learning tools from their own course material. Developed by Equanimity Labs.