CODE_OF_CONDUCT.rst
CONTRIBUTING.rst
LICENSE.md
MANIFEST.in
README.rst
pyproject.toml
setup.cfg
setup.py
src/scphylo/__init__.py
src/scphylo/commands/__init__.py
src/scphylo/commands/_cli.py
src/scphylo/commands/caller/_1rename.py
src/scphylo/commands/caller/_1sra.py
src/scphylo/commands/caller/_2fastp.py
src/scphylo/commands/caller/_3bwa.py
src/scphylo/commands/caller/_3star.py
src/scphylo/commands/caller/_4gatk.py
src/scphylo/commands/caller/_4rsem.py
src/scphylo/commands/caller/_5hapcaller.py
src/scphylo/commands/caller/_5mpileup.py
src/scphylo/commands/caller/_5mutect2.py
src/scphylo/commands/caller/_5sequenza.py
src/scphylo/commands/caller/_5strelka2.py
src/scphylo/commands/caller/_5varscan2.py
src/scphylo/commands/caller/_6bamreadcount.py
src/scphylo/commands/caller/_6bamsnap.py
src/scphylo/commands/caller/_6defuse.py
src/scphylo/commands/caller/_6pyclone.py
src/scphylo/commands/caller/_6snpeff.py
src/scphylo/commands/caller/_6varfilter.py
src/scphylo/commands/caller/_6vartrix.py
src/scphylo/commands/caller/__init__.py
src/scphylo/commands/caller/_pseudobulk.py
src/scphylo/commands/methyl/__init__.py
src/scphylo/commands/methyl/_builds.py
src/scphylo/commands/solver/__init__.py
src/scphylo/commands/solver/_bnb.py
src/scphylo/commands/solver/_booster.py
src/scphylo/commands/solver/_gpps.py
src/scphylo/commands/solver/_grmt.py
src/scphylo/commands/solver/_huntress.py
src/scphylo/commands/solver/_onconem.py
src/scphylo/commands/solver/_phiscs.py
src/scphylo/commands/solver/_scistree.py
src/scphylo/commands/solver/_scite.py
src/scphylo/commands/solver/_siclonefit.py
src/scphylo/commands/solver/_sphyr.py
src/scphylo/commands/utils/__init__.py
src/scphylo/commands/utils/_consensus.py
src/scphylo/commands/utils/_partf.py
src/scphylo/commands/utils/_score.py
src/scphylo/commands/utils/_search.py
src/scphylo/commands/utils/_trees.py
src/scphylo/datasets/__init__.py
src/scphylo/datasets/_datasets.py
src/scphylo/datasets/_simulate.py
src/scphylo/datasets/data/expression.h5ad.gz
src/scphylo/datasets/data/genotype.h5ad.gz
src/scphylo/datasets/real/acute_lymphocytic_leukemia1.h5ad
src/scphylo/datasets/real/acute_lymphocytic_leukemia2.h5ad
src/scphylo/datasets/real/acute_lymphocytic_leukemia3.h5ad
src/scphylo/datasets/real/acute_lymphocytic_leukemia4.h5ad
src/scphylo/datasets/real/acute_lymphocytic_leukemia5.h5ad
src/scphylo/datasets/real/acute_lymphocytic_leukemia6.h5ad
src/scphylo/datasets/real/acute_myeloid_leukemia1.h5ad
src/scphylo/datasets/real/acute_myeloid_leukemia2.h5ad
src/scphylo/datasets/real/colorectal1.h5ad
src/scphylo/datasets/real/colorectal2.h5ad
src/scphylo/datasets/real/colorectal2.rc.h5ad
src/scphylo/datasets/real/erbc.h5ad
src/scphylo/datasets/real/melanoma20.h5ad
src/scphylo/datasets/real/muscle_invasive_bladder.h5ad
src/scphylo/datasets/real/myeloproliferative_neoplasms18.h5ad
src/scphylo/datasets/real/myeloproliferative_neoplasms712.h5ad
src/scphylo/datasets/real/myeloproliferative_neoplasms78.h5ad
src/scphylo/datasets/real/oligodendroglioma_idh_mutated_tumor.h5ad
src/scphylo/datasets/real/ovarian.h5ad.gz
src/scphylo/datasets/real/renal_cell_carcinoma.h5ad
src/scphylo/datasets/real/tnbc.h5ad
src/scphylo/datasets/test/fp_0-fn_0-na_0.ground.CFMatrix
src/scphylo/datasets/test/fp_1-fn_0.1-na_0.bnb.CFMatrix
src/scphylo/datasets/test/test.tsv
src/scphylo/datasets/test/consensus/biorxiv.fig3b.CFMatrix
src/scphylo/datasets/test/consensus/biorxiv.fig3c.CFMatrix
src/scphylo/datasets/test/consensus/biorxiv.fig4b.CFMatrix
src/scphylo/datasets/test/consensus/biorxiv.fig4c.CFMatrix
src/scphylo/datasets/test/consensus/biorxiv.figs18a.CFMatrix
src/scphylo/datasets/test/consensus/recomb.fig1a.CFMatrix
src/scphylo/datasets/test/consensus/recomb.fig1b.CFMatrix
src/scphylo/datasets/test/input/T00.nwk
src/scphylo/datasets/test/input/T06.nwk
src/scphylo/datasets/test/output/test.siclonefit.score
src/scphylo/external/__init__.py
src/scphylo/external/_betabinom.py
src/scphylo/external/_mltd.cpp
src/scphylo/external/_mltd.pyx
src/scphylo/external/_mp3.py
src/scphylo/external/_scistree.cpp
src/scphylo/external/_scistree.pyx
src/scphylo/external/_scite.cpp
src/scphylo/external/_scite.pyx
src/scphylo/external/_scprob.cpp
src/scphylo/external/_scprob.pyx
src/scphylo/external/gpps/__init__.py
src/scphylo/external/gpps/_gpps_hc.py
src/scphylo/external/gpps/_gpps_ilp.py
src/scphylo/external/gpps/_nh2lgf.py
src/scphylo/external/gpps/_utils_hc.py
src/scphylo/external/gpps/_utils_ilp.py
src/scphylo/external/mltd/mltd.cpp
src/scphylo/external/mltd/mltd.h
src/scphylo/external/scistree/BinaryMatrix.cpp
src/scphylo/external/scistree/BinaryMatrix.h
src/scphylo/external/scistree/BioSequenceMatrix.cpp
src/scphylo/external/scistree/BioSequenceMatrix.h
src/scphylo/external/scistree/GenotypeMatrix.cpp
src/scphylo/external/scistree/GenotypeMatrix.h
src/scphylo/external/scistree/MarginalTree.cpp
src/scphylo/external/scistree/MarginalTree.h
src/scphylo/external/scistree/PhylogenyTree.cpp
src/scphylo/external/scistree/PhylogenyTree.h
src/scphylo/external/scistree/PhylogenyTreeBasic.cpp
src/scphylo/external/scistree/PhylogenyTreeBasic.h
src/scphylo/external/scistree/RBT.cpp
src/scphylo/external/scistree/RBT.h
src/scphylo/external/scistree/RerootTreeUtils.cpp
src/scphylo/external/scistree/RerootTreeUtils.h
src/scphylo/external/scistree/ScistDoublet.cpp
src/scphylo/external/scistree/ScistDoublet.hpp
src/scphylo/external/scistree/ScistErrRateInf.cpp
src/scphylo/external/scistree/ScistErrRateInf.hpp
src/scphylo/external/scistree/ScistGenotype.cpp
src/scphylo/external/scistree/ScistGenotype.hpp
src/scphylo/external/scistree/ScistPerfPhyImp.cpp
src/scphylo/external/scistree/ScistPerfPhyImp.hpp
src/scphylo/external/scistree/ScistPerfPhyUtils.cpp
src/scphylo/external/scistree/ScistPerfPhyUtils.hpp
src/scphylo/external/scistree/TreeBuilder.cpp
src/scphylo/external/scistree/TreeBuilder.h
src/scphylo/external/scistree/UnWeightedGraph.cpp
src/scphylo/external/scistree/UnWeightedGraph.h
src/scphylo/external/scistree/Utils.cpp
src/scphylo/external/scistree/Utils.h
src/scphylo/external/scistree/Utils2.cpp
src/scphylo/external/scistree/Utils2.h
src/scphylo/external/scistree/Utils3.cpp
src/scphylo/external/scistree/Utils3.h
src/scphylo/external/scistree/Utils4.cpp
src/scphylo/external/scistree/Utils4.h
src/scphylo/external/scistree/UtilsNumerical.cpp
src/scphylo/external/scistree/UtilsNumerical.h
src/scphylo/external/scistree/ctpl_stl.h
src/scphylo/external/scistree/main.cpp
src/scphylo/external/scistree/main.h
src/scphylo/external/scite/findBestTrees.cpp
src/scphylo/external/scite/findBestTrees.h
src/scphylo/external/scite/matrices.cpp
src/scphylo/external/scite/matrices.h
src/scphylo/external/scite/mcmc.cpp
src/scphylo/external/scite/mcmc.h
src/scphylo/external/scite/mcmcBinTreeMove.cpp
src/scphylo/external/scite/mcmcBinTreeMove.h
src/scphylo/external/scite/mcmcTreeMove.cpp
src/scphylo/external/scite/mcmcTreeMove.h
src/scphylo/external/scite/output.cpp
src/scphylo/external/scite/output.h
src/scphylo/external/scite/rand.cpp
src/scphylo/external/scite/rand.h
src/scphylo/external/scite/scoreBinTree.cpp
src/scphylo/external/scite/scoreBinTree.h
src/scphylo/external/scite/scoreTree.cpp
src/scphylo/external/scite/scoreTree.h
src/scphylo/external/scite/treelist.cpp
src/scphylo/external/scite/treelist.h
src/scphylo/external/scite/trees.cpp
src/scphylo/external/scite/trees.h
src/scphylo/external/scprob/main.cpp
src/scphylo/external/scprob/main.h
src/scphylo/io/__init__.py
src/scphylo/io/_genotype.py
src/scphylo/io/_tree.py
src/scphylo/logging/__init__.py
src/scphylo/logging/_logging.py
src/scphylo/pl/__init__.py
src/scphylo/pl/_data.py
src/scphylo/pl/_helper.py
src/scphylo/pl/_trees.py
src/scphylo/pp/__init__.py
src/scphylo/pp/_bifiltering.py
src/scphylo/pp/_binary.py
src/scphylo/pp/_readcount.py
src/scphylo/pp/_tree.py
src/scphylo/settings/__init__.py
src/scphylo/settings/_settings.py
src/scphylo/tl/__init__.py
src/scphylo/tl/cna/__init__.py
src/scphylo/tl/cna/_cna.py
src/scphylo/tl/consensus/__init__.py
src/scphylo/tl/consensus/_consensus.py
src/scphylo/tl/consensus/_consensus_day.py
src/scphylo/tl/fitch/__init__.py
src/scphylo/tl/fitch/_fitch.py
src/scphylo/tl/partition_function/__init__.py
src/scphylo/tl/partition_function/_clt_sampler.py
src/scphylo/tl/partition_function/_partition_function.py
src/scphylo/tl/partition_function/_pf.py
src/scphylo/tl/score/__init__.py
src/scphylo/tl/score/_others.py
src/scphylo/tl/score/_ours.py
src/scphylo/tl/solver/__init__.py
src/scphylo/tl/solver/_bnb.py
src/scphylo/tl/solver/_cardelino.py
src/scphylo/tl/solver/_cellphy.py
src/scphylo/tl/solver/_dendro.py
src/scphylo/tl/solver/_gpps.py
src/scphylo/tl/solver/_grmt.py
src/scphylo/tl/solver/_onconem.py
src/scphylo/tl/solver/_phiscs.py
src/scphylo/tl/solver/_sasc.py
src/scphylo/tl/solver/_sbm.py
src/scphylo/tl/solver/_scelestial.py
src/scphylo/tl/solver/_sciphi.py
src/scphylo/tl/solver/_scistree.py
src/scphylo/tl/solver/_scite.py
src/scphylo/tl/solver/_siclonefit.py
src/scphylo/tl/solver/_sphyr.py
src/scphylo/tl/solver/booster/__init__.py
src/scphylo/tl/solver/booster/_booster.py
src/scphylo/tl/solver/booster/_dependencies.py
src/scphylo/tl/solver/booster/_reconstruct_big_tree.py
src/scphylo/tl/solver/booster/_subsamples.py
src/scphylo/tl/solver/huntress/__init__.py
src/scphylo/tl/solver/huntress/_huntress.py
src/scphylo/ul/__init__.py
src/scphylo/ul/_caller.py
src/scphylo/ul/_hclustering.py
src/scphylo/ul/_packages.py
src/scphylo/ul/_servers.py
src/scphylo/ul/_trees.py
src/scphylo/ul/_utils.py
src/scphylo/ul/bamreadcount.py
src/scphylo/ul/cyvcf.py
src/scphylo/ul/rsem.py
src/scphylo/ul/sequenza.R
src/scphylo/ul/star.py
src/scphylo_tools.egg-info/PKG-INFO
src/scphylo_tools.egg-info/SOURCES.txt
src/scphylo_tools.egg-info/dependency_links.txt
src/scphylo_tools.egg-info/entry_points.txt
src/scphylo_tools.egg-info/requires.txt
src/scphylo_tools.egg-info/top_level.txt