This repository stores UShER phylogenetic trees for viral RefSeqs that have at least 1000 associated INSDC/GenBank sequences, limited to trees with at least 100 near-full-length alignable sequences. The trees are 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:
- tree.jsonl.gz: Taxonium tree file, viewable using https://taxonium.org/
- viz.nwk.gz: tree in Newick format; tip names include isolate, accession, collection date
- viz.pb.gz: tree in UShER protobuf format; tip names include isolate, accession, collection date
- optimized.pb.gz: tree in UShER protobuf format; tip names are INSDC/GenBank accessions
- output_stats.tsv: summary of sequence counts (available, filtered, aligned, in final tree)
- metadata.tsv.gz: metadata file describing input sequences in TSV format
Each pathogen subdirectory of trees also has a file config.toml that contains configuration parameters for the viral_usher build.