.gitignore
CONTRIBUTING.md
LICENSE
README.md
pyproject.toml
.github/workflows/docs.yml
doc/Makefile
doc/make.bat
doc/requirements.in
doc/requirements.txt
doc/changelog/CHANGELOG_0.1.0.md
doc/source/conf.py
doc/source/index.rst
doc/source/_static/custom.css
doc/source/api/index.rst
doc/source/user_guide/common_workflow.md
doc/source/user_guide/index.rst
doc/source/user_guide/overview.md
doc/source/user_guide/supported_datasets.md
mutcleaner/__init__.py
mutcleaner.egg-info/PKG-INFO
mutcleaner.egg-info/SOURCES.txt
mutcleaner.egg-info/dependency_links.txt
mutcleaner.egg-info/requires.txt
mutcleaner.egg-info/top_level.txt
mutcleaner/cleaners/__init__.py
mutcleaner/cleaners/antitoxin_pard3_cleaner.py
mutcleaner/cleaners/antitoxin_pard3_custom_cleaners.py
mutcleaner/cleaners/archstabms_1e10_cleaner.py
mutcleaner/cleaners/archstabms_1e10_custom_cleaners.py
mutcleaner/cleaners/base_config.py
mutcleaner/cleaners/basic_cleaners.py
mutcleaner/cleaners/cdna_proteolysis_cleaner.py
mutcleaner/cleaners/cdna_proteolysis_custom_cleaners.py
mutcleaner/cleaners/ctxm_cleaner.py
mutcleaner/cleaners/ddg_dtm_cleaners.py
mutcleaner/cleaners/human_domainome_custom_cleaners.py
mutcleaner/cleaners/human_domainome_sup2_cleaner.py
mutcleaner/cleaners/human_myoglobin_cleaner.py
mutcleaner/cleaners/human_myoglobin_custom_cleaners.py
mutcleaner/cleaners/proteingym_dms_substitutions_cleaner.py
mutcleaner/cleaners/proteingym_dms_substitutions_custom_cleaners.py
mutcleaner/cleaners/rbd_ace2_cleaner.py
mutcleaner/cleaners/rbd_antibody_cleaner.py
mutcleaner/cleaners/rbd_custom_cleaner.py
mutcleaner/cleaners/trpb_cleaner.py
mutcleaner/core/__init__.py
mutcleaner/core/alphabet.py
mutcleaner/core/codon.py
mutcleaner/core/constants.py
mutcleaner/core/dataset.py
mutcleaner/core/mutation.py
mutcleaner/core/pipeline.py
mutcleaner/core/sequence.py
mutcleaner/core/types.py
mutcleaner/utils/__init__.py
mutcleaner/utils/cleaner_workers.py
mutcleaner/utils/data_source.py
mutcleaner/utils/dataset_builders.py
mutcleaner/utils/label_resolvers.py
mutcleaner/utils/mutation_converter.py
mutcleaner/utils/raw_data_downloader.py
mutcleaner/utils/sequence_io.py
mutcleaner/utils/type_converter.py
tests/test_dataset.py
tests/test_mutation.py
tests/test_pipeline.py
tests/test_sequence.py
tools/changelog.py
tools/generate_changelog.sh
tools/release.sh