.gitignore
CONTRIBUTING.rst
HISTORY.rst
LICENSE
MANIFEST.in
README.md
requirements.txt
requirements_dev.txt
setup.cfg
setup.py
tox.ini
docs/.DS_Store
docs/Makefile
docs/README.md
docs/conf.py
docs/contributing.rst
docs/history.rst
docs/index.rst
docs/installation.rst
docs/make.bat
docs/api/gpvolve.analysis.pathways.rst
docs/api/gpvolve.cluster.base.rst
docs/api/gpvolve.cluster.from_paths.rst
docs/api/gpvolve.cluster.pcca.rst
docs/api/gpvolve.cluster.utils.rst
docs/api/gpvolve.fitness.rst
docs/api/gpvolve.fixation.rst
docs/api/gpvolve.flux.rst
docs/api/gpvolve.markovmodel.rst
docs/api/gpvolve.paths.rst
docs/api/gpvolve.utils.rst
docs/api/gpvolve.visualization.rst
docs/api/main.rst
docs/img/basic_example.png
docs/img/comp_pipeline.png
docs/img/path_analysis.png
docs/img/pcca_ordering.png
docs/img/pcca_tm.png
docs/img/tpt_output.png
docs/pages/fixation.rst
docs/pages/installation.rst
docs/pages/pipeline.rst
docs/pages/selection.rst
examples/Introduction to gpvolve.ipynb
examples/Second example.ipynb
gpvolve/.DS_Store
gpvolve/__init__.py
gpvolve/__version__.py
gpvolve/fitness.py
gpvolve/fixation.py
gpvolve/flux.py
gpvolve/markovmodel.py
gpvolve/paths.py
gpvolve/utils.py
gpvolve/visualization.py
gpvolve.egg-info/PKG-INFO
gpvolve.egg-info/SOURCES.txt
gpvolve.egg-info/dependency_links.txt
gpvolve.egg-info/requires.txt
gpvolve.egg-info/top_level.txt
gpvolve/analysis/pathways.py
gpvolve/cluster/base.py
gpvolve/cluster/from_paths.py
gpvolve/cluster/pcca.py
gpvolve/cluster/utils.py
tests/test_gpvolve.py