taxoniumtools

Taxonium tools

Taxonium tools is a Python utility that allows you to generate Taxonium format files from UShER mutation-annoated trees.

Installation

pip install taxoniumtools

Usage

Basic run

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

Use Chronumental to infer a time tree

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