├── BuildTree ├── BuildTree.py ├── BuildTreeEngine.py ├── CellPopulation.py ├── CellPopulationEngine.py ├── ClusterObject.py ├── ClusteringResults.py ├── Node.py ├── ShuffleMutations.py ├── Tree.py └── __init__.py ├── Cluster ├── Cluster.py ├── ClusterEngine.py ├── DpEngine.py └── __init__.py ├── Dockerfile ├── ExampleData ├── ExampleSamples │ ├── MySimulation_0.txt │ ├── MySimulation_1.txt │ ├── MySimulation_2.txt │ ├── MySimulation_3.txt │ ├── MySimulation_input.sif │ └── MySimulation_report.pdf └── Simulations │ ├── ExampleTreatment.txt │ ├── Example_Clust_File.txt │ ├── Example_CovFile.txt │ ├── Example_PurityFile.txt │ └── Example_SegFile.txt ├── ExampleRuns ├── Example_1D.phylogic_report.html ├── Example_ND.phylogic_report.html ├── PhylogicNDT-Example.ipynb └── PhylogicNDT-PhylogicSim.ipynb ├── GrowthKinetics ├── GrowthKinetics.py ├── GrowthKineticsEngine.py └── __init__.py ├── LICENSE ├── LeagueModel ├── LeagueModel.py ├── LeagueModelData.py └── __init__.py ├── PhylogicNDT.py ├── PhylogicSim ├── SimEngine.py ├── Simulations.py └── __init__.py ├── README.md ├── SinglePatientTiming ├── SinglePatientTiming.py ├── TimingEngine.py └── __init__.py ├── data ├── CorrectBias.py ├── Enums.py ├── Patient.py ├── Sample.py ├── SomaticEvents.py ├── __init__.py └── supplement_data │ ├── Blacklist_SNVs.txt │ ├── Driver_genes_v1.0.txt │ └── cytoBand.txt ├── output ├── PhylogicOutput.py ├── __init__.py ├── report_template.html_ └── timing_report_template.html_ ├── req └── utils ├── __init__.py ├── calc_ccf.py └── rdata_extractor.R /BuildTree/BuildTree.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/broadinstitute/PhylogicNDT/HEAD/BuildTree/BuildTree.py -------------------------------------------------------------------------------- /BuildTree/BuildTreeEngine.py: -------------------------------------------------------------------------------- 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