.gitignore
CHANGELOG.md
LICENSE
README.md
make_test_data.py
prek.toml
pyproject.toml
uv.lock
.github/workflows/docs.yml
.github/workflows/integration.yml
.github/workflows/lint.yml
.github/workflows/tests.yml
.github/workflows/wheels.yml
docs/CHANGELOG.md
docs/Makefile
docs/_config.yml
docs/_toc.yml
docs/alignments_analysis.md
docs/api.md
docs/arg_analysis.md
docs/build.sh
docs/cli.md
docs/development.md
docs/example_config.toml
docs/inference.md
docs/installation.md
docs/intro.md
docs/make_sc2ts_arg_subset.py
docs/make_viridian_subset.py
docs/sc2ts.png
docs/sc2ts_viridian_v1.2_subset_1000.trees.tsz
docs/viridian_mafft_subset_1000_v1.vcz.zip
notebooks/qc-template.ipynb
notebooks/test_ts.ipynb
sc2ts/__init__.py
sc2ts/__main__.py
sc2ts/_version.py
sc2ts/cli.py
sc2ts/core.py
sc2ts/data_import.py
sc2ts/dataset.py
sc2ts/debug.py
sc2ts/inference.py
sc2ts/jit.py
sc2ts/stats.py
sc2ts/tree_ops.py
sc2ts/validation.py
sc2ts.egg-info/PKG-INFO
sc2ts.egg-info/SOURCES.txt
sc2ts.egg-info/dependency_links.txt
sc2ts.egg-info/entry_points.txt
sc2ts.egg-info/requires.txt
sc2ts.egg-info/top_level.txt
sc2ts/data/annotation.csv
sc2ts/data/reference.fasta
tests/conftest.py
tests/sc2ts_fixtures.py
tests/test_api.py
tests/test_cli.py
tests/test_dataset.py
tests/test_debug.py
tests/test_inference.py
tests/test_jit.py
tests/test_tree_ops.py
tests/util.py
tests/data/.gitignore
tests/data/alignments-mafft.fasta.gz
tests/data/alignments.fasta.gz
tests/data/ba2_recomb.ts
tests/data/coalesce_mutations_time_bug.trees
tests/data/make_ba2_recomb.py
tests/data/metadata.tsv
tests/data/raw_viridian_metadata.tsv.gz
tests/data/testrun-conf.toml
tests/data/v0.1_dataset_ex.vcz.zip
tests/data/v0.1_output_ex.ts.tsz