LICENSE
README.md
pyproject.toml
setup.py
src/marker_alignments/__init__.py
src/marker_alignments/main.py
src/marker_alignments/mcl.py
src/marker_alignments/pysam2.py
src/marker_alignments/refdb_pattern.py
src/marker_alignments/store.py
src/marker_alignments/write.py
src/marker_alignments.egg-info/PKG-INFO
src/marker_alignments.egg-info/SOURCES.txt
src/marker_alignments.egg-info/dependency_links.txt
src/marker_alignments.egg-info/entry_points.txt
src/marker_alignments.egg-info/requires.txt
src/marker_alignments.egg-info/top_level.txt
tests/test_mcl.py
tests/test_parse_args.py
tests/test_read_alignments.py
tests/test_refdb_pattern.py
tests/test_store_counting.py
tests/test_store_filter.py
tests/test_store_transform_taxa.py