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CITATION.cff
CODE_OF_CONDUCT.rst
LICENSE
MANIFEST.in
Makefile
README.rst
pyproject.toml
requirements.txt
setup.cfg
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docs/requirements.txt
examples/README.rst
examples/reconstruction/README.rst
examples/reconstruction/compute_booster.py
tests/__init__.py
tests/_helpers.py
tests/test_commands.py
tests/test_datasets.py
tests/test_io.py
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tests/test_pl.py
tests/test_pp.py
tests/test_tl_consensus.py
tests/test_tl_partition_function.py
tests/test_tl_scores.py
tests/test_tl_solvers.py
tests/test_tl_solvers_tmp.py
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trisicell/commands/mcalling/s10velocitying.py
trisicell/commands/mcalling/z01status.py
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trisicell/external/_mltd.cpp
trisicell/external/_mltd.pyx
trisicell/external/_mp3.py
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trisicell/external/_scistree.pyx
trisicell/external/_scite.cpp
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trisicell/external/_scprob.pyx
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trisicell/external/scistree/BioSequenceMatrix.cpp
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trisicell/external/scistree/GenotypeMatrix.cpp
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trisicell/external/scistree/ScistGenotype.cpp
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trisicell/external/scite/treelist.cpp
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trisicell/io/_tree.py
trisicell/logging/__init__.py
trisicell/logging/_logging.py
trisicell/pl/__init__.py
trisicell/pl/_data.py
trisicell/pl/_helper.py
trisicell/pl/_trees.py
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trisicell/pp/_bifiltering.py
trisicell/pp/_binary.py
trisicell/pp/_readcount.py
trisicell/pp/_tree.py
trisicell/settings/__init__.py
trisicell/settings/_settings.py
trisicell/tl/__init__.py
trisicell/tl/cna/__init__.py
trisicell/tl/cna/_cna.py
trisicell/tl/consensus/__init__.py
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trisicell/tl/consensus/_consensus_day.py
trisicell/tl/fitch/__init__.py
trisicell/tl/fitch/_fitch.py
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trisicell/tl/partition_function/_partition_function.py
trisicell/tl/partition_function/_pf.py
trisicell/tl/score/__init__.py
trisicell/tl/score/_others.py
trisicell/tl/score/_ours.py
trisicell/tl/solver/__init__.py
trisicell/tl/solver/_bnb.py
trisicell/tl/solver/_cardelino.py
trisicell/tl/solver/_cellphy.py
trisicell/tl/solver/_dendro.py
trisicell/tl/solver/_gpps.py
trisicell/tl/solver/_grmt.py
trisicell/tl/solver/_onconem.py
trisicell/tl/solver/_phiscs.py
trisicell/tl/solver/_sasc.py
trisicell/tl/solver/_sbm.py
trisicell/tl/solver/_scelestial.py
trisicell/tl/solver/_sciphi.py
trisicell/tl/solver/_scistree.py
trisicell/tl/solver/_scite.py
trisicell/tl/solver/_siclonefit.py
trisicell/tl/solver/_sphyr.py
trisicell/tl/solver/booster/__init__.py
trisicell/tl/solver/booster/_booster.py
trisicell/tl/solver/booster/_dependencies.py
trisicell/tl/solver/booster/_reconstruct_big_tree.py
trisicell/tl/solver/booster/_subsamples.py
trisicell/tl/solver/huntress/__init__.py
trisicell/tl/solver/huntress/_huntress.py
trisicell/ul/__init__.py
trisicell/ul/_hclustering.py
trisicell/ul/_packages.py
trisicell/ul/_servers.py
trisicell/ul/_trees.py
trisicell/ul/_utils.py