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1. InfluenzaAReferenceDB InfluenzaAReferenceDBPublic

   This repo contains a script for generating a minimum index of all influenza A subtypes to use to annotate influenza A data with subtype for Genspectrum

   Jupyter Notebook 3

2. TreeAlgs-Fork TreeAlgs-ForkPublic

   Forked from PierreBarrat/TreeAlgs

   TreeAlgs fork for experimenting with ARG simulations

   Julia

3. augur augurPublic

   Forked from nextstrain/augur

   Pipeline components for real-time phylodynamic analysis

   Python

4. nextclade nextcladePublic

   Forked from nextstrain/nextclade

   Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

   Rust

5. ML_TreeBuilder_Review ML_TreeBuilder_ReviewPublic

   Repository where I evaluate the performance of the ML Tree Builder PhyloFormer on simulated Influenza Data

   Jupyter Notebook

6. MTKTools MTKToolsPublic

   This package contains methods for testing the accuracy of the MultiTreeKnit module of TreeKnit.jl

   Jupyter Notebook 1