This repository stores UShER phylogenetic trees for common viral pathogens, built by viral_usher and automatically updated on a monthly basis.
All tree files are in the trees directory, with a subdirectory per pathogen.
Each subdirectory contains the following files:
- optimized.pb.gz: tree in UShER protobuf format; tip names are GenBank accessions
- viz.pb.gz: tree in UShER protobuf format; tip names include isolate, accession, collection date
- metadata.tsv.gz: metadata file describing input sequences in TSV format
- tree.jsonl.gz: Taxonium tree file, viewable using https://taxonium.org/
Each pathogen subdirectory of trees also has a file config.toml that contains configuration parameters for the viral_usher build.