Library for dealing with phylogenetic trees in the NexSON format
nexson is a package for handling the “NexSON” format used by the Open Tree of Life project to store information about externally produced phylognetic trees. The package was refactored from peyotl, which is a more general purpose package.
python3 -mvenv env source env/bin/activate pip install -r requirements.txt python setup.py develop python setup.py test
performs the basic installation and test.
nexson is primarily written by Mark Holder, Emily Jane McTavish, and Jim Allman, but see the CONTRIBUTORS file for a more complete list of people who have contributed code.
Jim Allman, Karen Cranston, Cody Hinchliff, Mark Holder, Peter Midford, and Jonathon Rees all participated in the discussions that led to the NexSON mapping.
- The peyotl/test/data/nexson/phenoscape/nexml test file is from
https://raw.github.com/phenoscape/phenoscape-data/master/Curation%20Files/completed-phenex-files/Characiformes/Buckup_1998.xml Phenoscape file (download), NESCent [Feb 16, 2014] The citation for the data is in the nexml doc itself.
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