.gitignore
LICENSE
README.md
get_problematic_sites.sh
pyproject.toml
setup.cfg
setup.py
notebooks/RecombinantAncestry.ipynb
notebooks/lineage-graphs.ipynb
notebooks/lineage-imputation.ipynb
notebooks/qc-template.ipynb
sc2ts/__init__.py
sc2ts/__main__.py
sc2ts/_version.py
sc2ts/alignments.py
sc2ts/buildtree.py
sc2ts/cli.py
sc2ts/core.py
sc2ts/inference.py
sc2ts/lineages.py
sc2ts/local_tree.py
sc2ts/metadata.py
sc2ts/nextstrain.py
sc2ts/utils.py
sc2ts.egg-info/PKG-INFO
sc2ts.egg-info/SOURCES.txt
sc2ts.egg-info/dependency_links.txt
sc2ts.egg-info/not-zip-safe
sc2ts.egg-info/requires.txt
sc2ts.egg-info/top_level.txt
sc2ts/data/annotation.csv
sc2ts/data/problematic_sites.txt
sc2ts/data/reference.fasta
tests/test_convert.py
tests/test_extend.py
tests/test_inference.py
tests/test_utils.py
tests/util.py