GBIF-biodiverse-OpenTree

Linking data between GBIF, Biodiverse, and Open Tree of Life

The python scripts will rely on opentree and Dendropy. To set up a virtual environment and install them run:

virtualenv -p python3 venv-gbot
source venv-gbot/bin/activate
pip install -r requirements.txt

Once that is set up - you can reactivate using any time you want to run analyses

source venv-gbot/bin/activate

To get an induced subtree from synth for a set of opentree ids:

python scripts/induced_synth_subtree_from_csv.py -q tests/query.csv