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1. InfluenzaAReferenceDB InfluenzaAReferenceDB Public

   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. WISE-mut-freq-data-uploader WISE-mut-freq-data-uploader Public

   This repo includes a script to upload waste water virus mutation frequency data, produced by pangolin automation running v-pipe.

   Python 1

3. TreeAlgs-Fork TreeAlgs-Fork Public

   Forked from PierreBarrat/TreeAlgs

   TreeAlgs fork for experimenting with ARG simulations

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4. augur augur Public

   Forked from nextstrain/augur

   Pipeline components for real-time phylodynamic analysis

   Python

5. nextclade nextclade Public

   Forked from nextstrain/nextclade

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

   TypeScript

6. ML_TreeBuilder_Review ML_TreeBuilder_Review Public

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

   Jupyter Notebook