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Library for dealing with phylogenetic trees in the NexSON format

Project description

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.

Instructions

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.

Thanks

Thanks to NSF and HITS for funding support.

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.

Project details


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Files for nexson, version 0.0.4
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