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.gitignore
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CONTRIBUTING.rst
LICENSE
MANIFEST.in
Makefile
README.rst
pyproject.toml
requirements.txt
setup.cfg
setup.py
docs/requirements.txt
examples/README.rst
examples/assessment/README.rst
examples/assessment/compute_partf.py
examples/comparison/README.rst
examples/comparison/compute_ad.py
examples/comparison/compute_caset.py
examples/comparison/compute_disc.py
examples/comparison/compute_dl.py
examples/comparison/compute_gs.py
examples/comparison/compute_mltd.py
examples/comparison/compute_mp3.py
examples/comparison/compute_rf.py
examples/comparison/compute_tpted.py
examples/reconstruction/README.rst
examples/reconstruction/compute_bnb.py
examples/reconstruction/compute_booster.py
examples/reconstruction/compute_gpps.py
examples/reconstruction/compute_onconem.py
examples/reconstruction/compute_phiscs.py
examples/reconstruction/compute_scistree.py
examples/reconstruction/compute_scite.py
examples/reconstruction/compute_siclonefit.py
examples/reconstruction/compute_sphyr.py
examples/visualization/README.rst
examples/visualization/plot_clonal.py
examples/visualization/plot_dendrogram.py
scphylo/__init__.py
scphylo/commands/__init__.py
scphylo/commands/scphylo.py
scphylo/commands/caller/_1rename.py
scphylo/commands/caller/_1sra.py
scphylo/commands/caller/_2fastp.py
scphylo/commands/caller/_3bwa.py
scphylo/commands/caller/_3star.py
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scphylo/commands/caller/_5hapcaller.py
scphylo/commands/caller/_5mpileup.py
scphylo/commands/caller/_5mutect2.py
scphylo/commands/caller/_5sequenza.py
scphylo/commands/caller/_5strelka2.py
scphylo/commands/caller/_5varscan2.py
scphylo/commands/caller/_6bamreadcount.py
scphylo/commands/caller/_6bamsnap.py
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scphylo/commands/caller/_6pyclone.py
scphylo/commands/caller/_6snpeff.py
scphylo/commands/caller/_6varfilter.py
scphylo/commands/caller/_6vartrix.py
scphylo/commands/caller/__init__.py
scphylo/commands/caller/_pseudobulk.py
scphylo/commands/methyl/__init__.py
scphylo/commands/methyl/_builds.py
scphylo/commands/solver/__init__.py
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scphylo/datasets/__init__.py
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scphylo/datasets/_simulate.py
scphylo/datasets/data/expression.h5ad.gz
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scphylo/datasets/real/acute_lymphocytic_leukemia2.h5ad
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scphylo/datasets/real/acute_lymphocytic_leukemia4.h5ad
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scphylo/datasets/real/acute_lymphocytic_leukemia6.h5ad
scphylo/datasets/real/acute_myeloid_leukemia1.h5ad
scphylo/datasets/real/acute_myeloid_leukemia2.h5ad
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scphylo/datasets/real/melanoma20.h5ad
scphylo/datasets/real/muscle_invasive_bladder.h5ad
scphylo/datasets/real/myeloproliferative_neoplasms18.h5ad
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scphylo/datasets/real/myeloproliferative_neoplasms78.h5ad
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scphylo/datasets/test/consensus/biorxiv.fig3b.CFMatrix
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scphylo/datasets/test/consensus/recomb.fig1a.CFMatrix
scphylo/datasets/test/consensus/recomb.fig1b.CFMatrix
scphylo/datasets/test/input/T00.nwk
scphylo/datasets/test/input/T06.nwk
scphylo/datasets/test/output/test.siclonefit.score
scphylo/external/__init__.py
scphylo/external/_betabinom.py
scphylo/external/_mltd.cpp
scphylo/external/_mltd.pyx
scphylo/external/_mp3.py
scphylo/external/_scistree.cpp
scphylo/external/_scistree.pyx
scphylo/external/_scite.cpp
scphylo/external/_scite.pyx
scphylo/external/_scprob.cpp
scphylo/external/_scprob.pyx
scphylo/external/gpps/__init__.py
scphylo/external/gpps/_gpps_hc.py
scphylo/external/gpps/_gpps_ilp.py
scphylo/external/gpps/_nh2lgf.py
scphylo/external/gpps/_utils_hc.py
scphylo/external/gpps/_utils_ilp.py
scphylo/external/mltd/mltd.cpp
scphylo/external/mltd/mltd.h
scphylo/external/scistree/BinaryMatrix.cpp
scphylo/external/scistree/BinaryMatrix.h
scphylo/external/scistree/BioSequenceMatrix.cpp
scphylo/external/scistree/BioSequenceMatrix.h
scphylo/external/scistree/GenotypeMatrix.cpp
scphylo/external/scistree/GenotypeMatrix.h
scphylo/external/scistree/MarginalTree.cpp
scphylo/external/scistree/MarginalTree.h
scphylo/external/scistree/PhylogenyTree.cpp
scphylo/external/scistree/PhylogenyTree.h
scphylo/external/scistree/PhylogenyTreeBasic.cpp
scphylo/external/scistree/PhylogenyTreeBasic.h
scphylo/external/scistree/RBT.cpp
scphylo/external/scistree/RBT.h
scphylo/external/scistree/RerootTreeUtils.cpp
scphylo/external/scistree/RerootTreeUtils.h
scphylo/external/scistree/ScistDoublet.cpp
scphylo/external/scistree/ScistDoublet.hpp
scphylo/external/scistree/ScistErrRateInf.cpp
scphylo/external/scistree/ScistErrRateInf.hpp
scphylo/external/scistree/ScistGenotype.cpp
scphylo/external/scistree/ScistGenotype.hpp
scphylo/external/scistree/ScistPerfPhyImp.cpp
scphylo/external/scistree/ScistPerfPhyImp.hpp
scphylo/external/scistree/ScistPerfPhyUtils.cpp
scphylo/external/scistree/ScistPerfPhyUtils.hpp
scphylo/external/scistree/TreeBuilder.cpp
scphylo/external/scistree/TreeBuilder.h
scphylo/external/scistree/UnWeightedGraph.cpp
scphylo/external/scistree/UnWeightedGraph.h
scphylo/external/scistree/Utils.cpp
scphylo/external/scistree/Utils.h
scphylo/external/scistree/Utils2.cpp
scphylo/external/scistree/Utils2.h
scphylo/external/scistree/Utils3.cpp
scphylo/external/scistree/Utils3.h
scphylo/external/scistree/Utils4.cpp
scphylo/external/scistree/Utils4.h
scphylo/external/scistree/UtilsNumerical.cpp
scphylo/external/scistree/UtilsNumerical.h
scphylo/external/scistree/ctpl_stl.h
scphylo/external/scistree/main.cpp
scphylo/external/scistree/main.h
scphylo/external/scite/findBestTrees.cpp
scphylo/external/scite/findBestTrees.h
scphylo/external/scite/matrices.cpp
scphylo/external/scite/matrices.h
scphylo/external/scite/mcmc.cpp
scphylo/external/scite/mcmc.h
scphylo/external/scite/mcmcBinTreeMove.cpp
scphylo/external/scite/mcmcBinTreeMove.h
scphylo/external/scite/mcmcTreeMove.cpp
scphylo/external/scite/mcmcTreeMove.h
scphylo/external/scite/output.cpp
scphylo/external/scite/output.h
scphylo/external/scite/rand.cpp
scphylo/external/scite/rand.h
scphylo/external/scite/scoreBinTree.cpp
scphylo/external/scite/scoreBinTree.h
scphylo/external/scite/scoreTree.cpp
scphylo/external/scite/scoreTree.h
scphylo/external/scite/treelist.cpp
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scphylo/external/scite/trees.cpp
scphylo/external/scite/trees.h
scphylo/external/scprob/main.cpp
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scphylo/io/__init__.py
scphylo/io/_genotype.py
scphylo/io/_tree.py
scphylo/logging/__init__.py
scphylo/logging/_logging.py
scphylo/pl/__init__.py
scphylo/pl/_data.py
scphylo/pl/_helper.py
scphylo/pl/_trees.py
scphylo/pp/__init__.py
scphylo/pp/_bifiltering.py
scphylo/pp/_binary.py
scphylo/pp/_readcount.py
scphylo/pp/_tree.py
scphylo/settings/__init__.py
scphylo/settings/_settings.py
scphylo/tl/__init__.py
scphylo/tl/cna/__init__.py
scphylo/tl/cna/_cna.py
scphylo/tl/consensus/__init__.py
scphylo/tl/consensus/_consensus.py
scphylo/tl/consensus/_consensus_day.py
scphylo/tl/fitch/__init__.py
scphylo/tl/fitch/_fitch.py
scphylo/tl/partition_function/__init__.py
scphylo/tl/partition_function/_clt_sampler.py
scphylo/tl/partition_function/_partition_function.py
scphylo/tl/partition_function/_pf.py
scphylo/tl/score/__init__.py
scphylo/tl/score/_others.py
scphylo/tl/score/_ours.py
scphylo/tl/solver/__init__.py
scphylo/tl/solver/_bnb.py
scphylo/tl/solver/_cardelino.py
scphylo/tl/solver/_cellphy.py
scphylo/tl/solver/_dendro.py
scphylo/tl/solver/_gpps.py
scphylo/tl/solver/_grmt.py
scphylo/tl/solver/_onconem.py
scphylo/tl/solver/_phiscs.py
scphylo/tl/solver/_sasc.py
scphylo/tl/solver/_sbm.py
scphylo/tl/solver/_scelestial.py
scphylo/tl/solver/_sciphi.py
scphylo/tl/solver/_scistree.py
scphylo/tl/solver/_scite.py
scphylo/tl/solver/_siclonefit.py
scphylo/tl/solver/_sphyr.py
scphylo/tl/solver/booster/__init__.py
scphylo/tl/solver/booster/_booster.py
scphylo/tl/solver/booster/_dependencies.py
scphylo/tl/solver/booster/_reconstruct_big_tree.py
scphylo/tl/solver/booster/_subsamples.py
scphylo/tl/solver/huntress/__init__.py
scphylo/tl/solver/huntress/_huntress.py
scphylo/ul/__init__.py
scphylo/ul/_caller.py
scphylo/ul/_hclustering.py
scphylo/ul/_packages.py
scphylo/ul/_servers.py
scphylo/ul/_trees.py
scphylo/ul/_utils.py
scphylo/ul/bamreadcount.py
scphylo/ul/cyvcf.py
scphylo/ul/rsem.py
scphylo/ul/sequenza.R
scphylo/ul/star.py
scphylo_tools.egg-info/PKG-INFO
scphylo_tools.egg-info/SOURCES.txt
scphylo_tools.egg-info/dependency_links.txt
scphylo_tools.egg-info/entry_points.txt
scphylo_tools.egg-info/requires.txt
scphylo_tools.egg-info/top_level.txt
tests/__init__.py
tests/_helpers.py
tests/conftest.py
tests/test_commands_solver.py
tests/test_datasets.py
tests/test_io.py
tests/test_logging.py
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
tests/test_ul.py