CHANGELOG.md
LICENSE
MANIFEST.in
OUTPUT_GUIDE.md
README.md
pyproject.toml
requirements.txt
setup.py
docs/NEW_API_REFERENCE.md
examples/config_template.txt
examples/data/Primate.nex
examples/data/alignment.fas
examples/data/morpho.nex
examples/data/proteins.phy
examples/data/simple_test.nex
images/annotated_tree.png
images/site_hist_Clade_X.png
images/site_plot_Clade_X.png
pandecay/__init__.py
pandecay/cli.py
pandecay.egg-info/PKG-INFO
pandecay.egg-info/SOURCES.txt
pandecay.egg-info/dependency_links.txt
pandecay.egg-info/entry_points.txt
pandecay.egg-info/requires.txt
pandecay.egg-info/top_level.txt
pandecay/core/__init__.py
pandecay/core/analysis_engine.py
pandecay/core/configuration.py
pandecay/core/constants.py
pandecay/core/utils.py