Dockerfile
LICENSE
MANIFEST.in
README.md
environment.yml
pyproject.toml
docs/api.md
docs/cli.md
docs/conf.py
docs/getting_started.md
docs/index.md
docs/input_validation.md
docs/interpretation.md
docs/metrics.md
docs/requirements.txt
docs/assets/codonadaptpy_graphical_abstract.png
examples/basic_analysis.py
src/CodonAdaptPy.egg-info/PKG-INFO
src/CodonAdaptPy.egg-info/SOURCES.txt
src/CodonAdaptPy.egg-info/dependency_links.txt
src/CodonAdaptPy.egg-info/entry_points.txt
src/CodonAdaptPy.egg-info/requires.txt
src/CodonAdaptPy.egg-info/top_level.txt
src/codonadaptpy/__init__.py
src/codonadaptpy/__main__.py
src/codonadaptpy/__version__.py
src/codonadaptpy/aggregation.py
src/codonadaptpy/analyzer.py
src/codonadaptpy/cli.py
src/codonadaptpy/comparative.py
src/codonadaptpy/exceptions.py
src/codonadaptpy/genetic_code.py
src/codonadaptpy/models.py
src/codonadaptpy/optimizer.py
src/codonadaptpy/parsers.py
src/codonadaptpy/phylo_visualization.py
src/codonadaptpy/phylogenetics.py
src/codonadaptpy/py.typed
src/codonadaptpy/references.py
src/codonadaptpy/reporting.py
src/codonadaptpy/validation.py
src/codonadaptpy/visualization.py
src/codonadaptpy/metrics/__init__.py
src/codonadaptpy/metrics/adaptation.py
src/codonadaptpy/metrics/composition.py
src/codonadaptpy/metrics/evolutionary.py
src/codonadaptpy/metrics/host.py
src/codonadaptpy/metrics/pairs.py
src/codonadaptpy/metrics/usage.py
tests/test_aggregation.py
tests/test_analyzer.py
tests/test_comparative.py
tests/test_independent_validation_fixtures.py
tests/test_metrics.py
tests/test_optimizer.py
tests/test_parsers.py
tests/test_phylogenetics.py
tests/test_references_reporting_cli.py
tests/test_validation.py
tests/test_visualization.py