├── .bumpversion.cfg ├── .gitattributes ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── enhancement_request.md │ └── general_question.md ├── PULL_REQUEST_TEMPLATE.md └── workflows │ └── ci.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yml ├── .rstcheck.cfg ├── .scripts └── ci │ └── install.sh ├── CITATION.cff ├── CODE_OF_CONDUCT.rst ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.rst ├── docs ├── Makefile ├── make.bat ├── requirements.txt ├── requirements_rtfd.txt └── source │ ├── _static │ ├── css │ │ └── custom.css │ ├── images │ │ ├── badge_colab.svg │ │ ├── badge_nbviewer.svg │ │ ├── evolution.png │ │ ├── gatk.png │ │ ├── github_logo.svg │ │ ├── logo.svg │ │ ├── orcid_logo.svg │ │ ├── overview.png │ │ ├── trisicellboost.png │ │ ├── trisicellcons.png │ │ └── trisicellpartf.png │ └── thumbnails │ │ └── trisicell-boost.png │ ├── _templates │ └── autosummary │ │ ├── base.rst │ │ ├── class.rst │ │ └── function.rst │ ├── about.rst │ ├── api.rst │ ├── caller.rst │ ├── citing.rst │ ├── cli.rst │ ├── conf.py │ ├── example.ipynb │ ├── index.rst │ ├── installation.rst │ ├── references.bib │ ├── references.rst │ └── release_notes.rst ├── examples ├── README.rst └── reconstruction │ ├── README.rst │ └── compute_booster.py ├── pyproject.toml ├── requirements.txt ├── setup.cfg ├── setup.py ├── tests ├── __init__.py ├── _helpers.py ├── test_commands.py ├── test_datasets.py ├── test_io.py ├── test_logging.py ├── test_pl.py ├── test_pp.py ├── test_tl_consensus.py ├── test_tl_partition_function.py ├── test_tl_scores.py ├── test_tl_solvers.py ├── test_tl_solvers_tmp.py └── test_ul.py └── trisicell ├── __init__.py ├── commands ├── __init__.py ├── _bnb.py ├── _booster.py ├── _consensus.py ├── _gpps.py ├── _grmt.py ├── _huntress.py ├── _mcalling.py ├── _onconem.py ├── _partf.py ├── _phiscs.py ├── _scistree.py ├── _scite.py ├── _score.py ├── _search.py ├── _siclonefit.py ├── _sphyr.py ├── _trees.py ├── mcalling │ ├── __init__.py │ ├── s01indexing.py │ ├── s02mapping.py │ ├── s03indexing.py │ ├── s04mapping.py │ ├── s05calling.py │ ├── s06jointcalling.py │ ├── s07merging.py │ ├── s08annotating.py │ ├── s09expressing.py │ ├── s10velocitying.py │ ├── z01status.py │ ├── z02matrixing.py │ └── z03clean.py └── trisicell.py ├── datasets ├── __init__.py ├── _datasets.py ├── _simulate.py ├── data │ ├── expression.h5ad.gz │ └── genotype.h5ad.gz ├── real │ ├── colorectal2.h5ad │ ├── colorectal2.rc.h5ad │ └── ovarian.h5ad.gz └── test │ ├── T00.nwk │ ├── T06.nwk │ ├── consensus │ ├── biorxiv.fig3b.CFMatrix │ ├── biorxiv.fig3c.CFMatrix │ ├── biorxiv.fig4b.CFMatrix │ ├── biorxiv.fig4c.CFMatrix │ ├── biorxiv.figs18a.CFMatrix │ ├── recomb.fig1a.CFMatrix │ └── recomb.fig1b.CFMatrix │ ├── fp_0-fn_0-na_0.ground.CFMatrix │ ├── fp_1-fn_0.1-na_0.bnb.CFMatrix │ ├── mcalling │ ├── cell0_1.fastq.gz │ ├── cell0_2.fastq.gz │ ├── cell1_1.fastq.gz │ ├── cell1_2.fastq.gz │ ├── cell2_1.fastq.gz │ ├── cell2_2.fastq.gz │ ├── cell3_1.fastq.gz │ ├── cell3_2.fastq.gz │ ├── cell4_1.fastq.gz │ ├── cell4_2.fastq.gz │ ├── cell5_1.fastq.gz │ ├── cell5_2.fastq.gz │ ├── cell6_1.fastq.gz │ ├── cell6_2.fastq.gz │ ├── cell7_1.fastq.gz │ ├── cell7_2.fastq.gz │ ├── cell8_1.fastq.gz │ ├── cell8_2.fastq.gz │ ├── cell9_1.fastq.gz │ └── cell9_2.fastq.gz │ ├── mcalling_config.yml │ └── test.tsv ├── external ├── __init__.py ├── _betabinom.py ├── _mltd.cpp ├── _mltd.pyx ├── _mp3.py ├── _scistree.cpp ├── _scistree.pyx ├── _scite.cpp ├── _scite.pyx ├── _scprob.cpp ├── _scprob.pyx ├── gpps │ ├── __init__.py │ ├── _gpps_hc.py │ ├── _gpps_ilp.py │ ├── _nh2lgf.py │ ├── _utils_hc.py │ └── _utils_ilp.py ├── mltd │ ├── mltd.cpp │ └── mltd.h ├── scistree │ ├── BinaryMatrix.cpp │ ├── BinaryMatrix.h │ ├── BioSequenceMatrix.cpp │ ├── BioSequenceMatrix.h │ ├── GenotypeMatrix.cpp │ ├── GenotypeMatrix.h │ ├── MarginalTree.cpp │ ├── MarginalTree.h │ ├── PhylogenyTree.cpp │ ├── PhylogenyTree.h │ ├── PhylogenyTreeBasic.cpp │ ├── PhylogenyTreeBasic.h │ ├── RBT.cpp │ ├── RBT.h │ ├── RerootTreeUtils.cpp │ ├── RerootTreeUtils.h │ ├── ScistDoublet.cpp │ ├── ScistDoublet.hpp │ ├── ScistErrRateInf.cpp │ ├── ScistErrRateInf.hpp │ ├── ScistGenotype.cpp │ ├── ScistGenotype.hpp │ ├── ScistPerfPhyImp.cpp │ ├── ScistPerfPhyImp.hpp │ ├── ScistPerfPhyUtils.cpp │ ├── ScistPerfPhyUtils.hpp │ ├── TreeBuilder.cpp │ ├── TreeBuilder.h │ ├── UnWeightedGraph.cpp │ ├── UnWeightedGraph.h │ ├── Utils.cpp │ ├── Utils.h │ ├── Utils2.cpp │ ├── Utils2.h │ ├── Utils3.cpp │ ├── Utils3.h │ ├── Utils4.cpp │ ├── Utils4.h │ ├── UtilsNumerical.cpp │ ├── UtilsNumerical.h │ ├── ctpl_stl.h │ ├── main.cpp │ └── main.h ├── scite │ ├── findBestTrees.cpp │ ├── findBestTrees.h │ ├── matrices.cpp │ ├── matrices.h │ ├── mcmc.cpp │ ├── mcmc.h │ ├── mcmcBinTreeMove.cpp │ ├── mcmcBinTreeMove.h │ ├── mcmcTreeMove.cpp │ ├── mcmcTreeMove.h │ ├── output.cpp │ ├── output.h │ ├── rand.cpp │ ├── rand.h │ ├── scoreBinTree.cpp │ ├── scoreBinTree.h │ ├── scoreTree.cpp │ ├── scoreTree.h │ ├── treelist.cpp │ ├── treelist.h │ ├── trees.cpp │ └── trees.h └── scprob │ ├── main.cpp │ └── main.h ├── io ├── __init__.py ├── _genotype.py └── _tree.py ├── logging ├── __init__.py └── _logging.py ├── pl ├── __init__.py ├── _data.py ├── _helper.py └── _trees.py ├── pp ├── __init__.py ├── _bifiltering.py ├── _binary.py ├── _readcount.py └── _tree.py ├── settings ├── __init__.py └── _settings.py ├── tl ├── __init__.py ├── cna │ ├── __init__.py │ └── _cna.py ├── consensus │ ├── __init__.py │ ├── _consensus.py │ └── _consensus_day.py ├── fitch │ ├── __init__.py │ └── _fitch.py ├── partition_function │ ├── __init__.py │ ├── _clt_sampler.py │ ├── _partition_function.py │ └── _pf.py ├── score │ ├── __init__.py │ ├── _others.py │ └── _ours.py └── solver │ ├── __init__.py │ ├── _bnb.py │ ├── _cardelino.py │ ├── _cellphy.py │ ├── _dendro.py │ ├── _gpps.py │ ├── _grmt.py │ ├── _onconem.py │ ├── _phiscs.py │ ├── _sasc.py │ ├── _sbm.py │ ├── _scelestial.py │ ├── _sciphi.py │ ├── _scistree.py │ ├── _scite.py │ ├── _siclonefit.py 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