LICENSE.md
README.md
setup.py
clipkit/__init__.py
clipkit/__main__.py
clipkit/api.py
clipkit/args_processing.py
clipkit/clipkit.py
clipkit/exceptions.py
clipkit/files.py
clipkit/helpers.py
clipkit/logger.py
clipkit/modes.py
clipkit/msa.py
clipkit/parser.py
clipkit/settings.py
clipkit/site_classification.py
clipkit/smart_gap_helper.py
clipkit/stats.py
clipkit/version.py
clipkit/warnings.py
clipkit/write.py
clipkit.egg-info/PKG-INFO
clipkit.egg-info/SOURCES.txt
clipkit.egg-info/dependency_links.txt
clipkit.egg-info/entry_points.txt
clipkit.egg-info/requires.txt
clipkit.egg-info/top_level.txt
clipkit/ecomp/__init__.py
clipkit/ecomp/reader.py
clipkit/ecomp/writer.py
tests/__init__.py
tests/conftest.py
tests/integration/__init__.py
tests/integration/test_api.py
tests/integration/test_c3.py
tests/integration/test_codon.py
tests/integration/test_complementary_output.py
tests/integration/test_cst.py
tests/integration/test_ecomp_input.py
tests/integration/test_ends_only.py
tests/integration/test_gappy_mode.py
tests/integration/test_kpi_gappy_mode.py
tests/integration/test_kpi_mode.py
tests/integration/test_kpi_smart_gap_mode.py
tests/integration/test_kpic_gappy_mode.py
tests/integration/test_kpic_mode.py
tests/integration/test_kpic_smart_gap_mode.py
tests/integration/test_smart_gap_mode.py
tests/integration/test_writing_to_different_output_file_formats.py
tests/integration/test_writing_to_log_file.py
tests/unit/__init__.py
tests/unit/test_args_parsing.py
tests/unit/test_entrypoint.py
tests/unit/test_execution_state.py
tests/unit/test_files.py
tests/unit/test_msa.py
tests/unit/test_parallel.py
tests/unit/test_parallel_simple.py
tests/unit/test_parallel_standalone.py
tests/unit/test_parser.py
tests/unit/test_smart_gap_helper.py
tests/unit/test_thread_heuristics.py
tests/unit/test_warnings.py
tests/unit/ecomp/__init__.py
tests/unit/ecomp/test_reader.py