This folder contains versioned subdirectories of Open Tree of Life data, e.g. v16.1/. Each subdirectory is created by the download_opentree script and contains:
labelled_supertree_simplified_ottnames.tre-- the raw downloaded treedraftversion.tre-- the tree withmrca***labels removed and whitespace normalisedtaxonomy.tsv-- the OTT taxonomy file
These subdirectories are .gitignored and tracked by DVC as pipeline outputs.
Run the download script with the desired synthesis version:
download_opentree --version v16.1 --output-dir data/OpenTree
The script fetches the synthesis manifest to look up the correct OTT taxonomy version, then downloads both the labelled supertree and taxonomy automatically.
This is also available as a DVC pipeline stage (download_opentree in dvc.yaml), so dvc repro will run it when ot_version changes in params.yaml.
These files are processed by the pipeline stages in dvc.yaml to create the full OneZoom tree. The taxonomy.tsv file is also used by other stages (e.g. for popularity mapping, EoL filtering, etc.).
NB: for the rationale of using ...simplified_ottnames see
OpenTreeOfLife/treemachine#147 (comment) and also here