Taxonium tools is a Python utility that allows you to generate Taxonium format files from UShER mutation-annoated trees.
pip install taxoniumtools
First get some files:
wget https://github.com/theosanderson/taxonium/raw/master/taxoniumtools/test_data/tfci.meta.tsv.gz
wget https://raw.githubusercontent.com/theosanderson/taxonium/master/taxoniumtools/test_data/hu1.gb
wget https://github.com/theosanderson/taxonium/raw/master/taxoniumtools/test_data/tfci.pb
Then convert from UShER pb format to Taxonium jsonl format:
usher_to_taxonium --input tfci.pb --output tfci-taxonium.jsonl.gz --metadata tfci.meta.tsv.gz --genbank hu1.gb \
--columns genbank_accession,country,date,pangolin_lineage
You can then open that tfci-taxonium.jsonl.gz file at taxonium.org
Taxonium tools can also use Chronumental to infer a time tree for the phylogeny.
pip install chronumental
usher_to_taxonium --input tfci.pb --output tfci-taxonium.jsonl.gz --metadata tfci.meta.tsv.gz --genbank hu1.gb \
--columns genbank_accession,country,date,pangolin_lineage --chronumental --chronumental_steps 300