.gitignore
.pre-commit-config.yaml
.ruff.toml
CONTRIBUTING.md
LICENSE
MANIFEST.in
Makefile
README.md
pyproject.toml
requirements.txt
setup.py
.github/workflows/lint.yml
.github/workflows/tests.yml
drhip/__init__.py
drhip/cli.py
drhip/config.py
drhip/version.py
drhip.egg-info/PKG-INFO
drhip.egg-info/SOURCES.txt
drhip.egg-info/dependency_links.txt
drhip.egg-info/entry_points.txt
drhip.egg-info/not-zip-safe
drhip.egg-info/requires.txt
drhip.egg-info/top_level.txt
drhip/methods/__init__.py
drhip/methods/base.py
drhip/methods/busted.py
drhip/methods/cfel.py
drhip/methods/fel.py
drhip/methods/meme.py
drhip/methods/prime.py
drhip/methods/registry.py
drhip/methods/relax.py
drhip/parsers/__init__.py
drhip/parsers/process_gene.py
drhip/utils/__init__.py
drhip/utils/file_handlers.py
drhip/utils/result_helpers.py
drhip/utils/sequence_utils.py
drhip/utils/tree_helpers.py
tests/__init__.py
tests/conftest.py
tests/test_all_methods_site_indexing.py
tests/test_cfel_Beta_and_Qvalue_updates.py
tests/test_cfel_backward_compatibility.py
tests/test_cfel_comparison_outputs.py
tests/test_cli.py
tests/test_file_handlers.py
tests/test_input_validation.py
tests/test_methods.py
tests/test_process_gene.py
tests/test_result_helpers.py
tests/test_sequence_utils.py
tests/test_tree_helpers.py
tests/data/hyphy/capsid_protein_C-nodups.fasta
tests/data/hyphy-comparisons/BUSTED/pretend_DENV1_ref.part_NC_001477.1__capsid_protein_C__95-394_DENV1.BUSTED.json
tests/data/hyphy-comparisons/BUSTED/pretend_DENV1_ref.part_NC_001477.1__membrane_glycoprotein.BUSTED.json
tests/data/hyphy-comparisons/CONTRASTFEL/pretend_DENV1_ref.part_NC_001477.1__capsid_protein_C__95-394_DENV1.CONTRASTFEL.json
tests/data/hyphy-comparisons/CONTRASTFEL/pretend_DENV1_ref.part_NC_001477.1__capsid_protein_C__95-394_DENV1.CONTRASTFEL.no-subs.json
tests/data/hyphy-comparisons/CONTRASTFEL/pretend_DENV1_ref.part_NC_001477.1__membrane_glycoprotein.CONTRASTFEL.json
tests/data/hyphy-comparisons/CONTRASTFEL/pretend_DENV1_ref.part_NC_001477.1__membrane_glycoprotein.CONTRASTFEL.no-subs.json
tests/data/hyphy-comparisons/FEL/pretend_DENV1_ref.part_NC_001477.1__capsid_protein_C__95-394_DENV1.FEL.json
tests/data/hyphy-comparisons/FEL/pretend_DENV1_ref.part_NC_001477.1__membrane_glycoprotein.FEL.json
tests/data/hyphy-comparisons/MEME/pretend_DENV1_ref.part_NC_001477.1__capsid_protein_C__95-394_DENV1.MEME.json
tests/data/hyphy-comparisons/MEME/pretend_DENV1_ref.part_NC_001477.1__membrane_glycoprotein.MEME.json
tests/data/hyphy-comparisons/PRIME/pretend_DENV1_ref.part_NC_001477.1__capsid_protein_C__95-394_DENV1.PRIME.json
tests/data/hyphy-comparisons/PRIME/pretend_DENV1_ref.part_NC_001477.1__membrane_glycoprotein.PRIME.json
tests/data/hyphy-comparisons/RELAX/pretend_DENV1_ref.part_NC_001477.1__capsid_protein_C__95-394_DENV1.RELAX.json
tests/data/hyphy-comparisons/RELAX/pretend_DENV1_ref.part_NC_001477.1__membrane_glycoprotein.RELAX.json
tests/data/hyphy/BUSTED/capsid_protein_C.BUSTED.json
tests/data/hyphy/FEL/capsid_protein_C.FEL.json
tests/data/hyphy/MEME/capsid_protein_C.MEME.json
tests/data/hyphy/PRIME/capsid_protein_C.PRIME.json