All modules for which code is available
- cassiopeia.critique.compare
- cassiopeia.data.CassiopeiaTree
- cassiopeia.data.utilities
- cassiopeia.plotting.itol_utilities
- cassiopeia.plotting.local
- cassiopeia.plotting.local_3d
- cassiopeia.preprocess.pipeline
- cassiopeia.preprocess.utilities
- cassiopeia.simulator.BirthDeathFitnessSimulator
- cassiopeia.simulator.BrownianSpatialDataSimulator
- cassiopeia.simulator.Cas9LineageTracingDataSimulator
- cassiopeia.simulator.ClonalSpatialDataSimulator
- cassiopeia.simulator.CompleteBinarySimulator
- cassiopeia.simulator.SimpleFitSubcloneSimulator
- cassiopeia.simulator.SpatialLeafSubsampler
- cassiopeia.simulator.SupercellularSampler
- cassiopeia.simulator.UniformLeafSubsampler
- cassiopeia.simulator.ecDNABirthDeathSimulator
- cassiopeia.solver.HybridSolver
- cassiopeia.solver.ILPSolver
- cassiopeia.solver.MaxCutGreedySolver
- cassiopeia.solver.MaxCutSolver
- cassiopeia.solver.NeighborJoiningSolver
- cassiopeia.solver.PercolationSolver
- cassiopeia.solver.SharedMutationJoiningSolver
- cassiopeia.solver.SpectralGreedySolver
- cassiopeia.solver.SpectralSolver
- cassiopeia.solver.UPGMASolver
- cassiopeia.solver.VanillaGreedySolver
- cassiopeia.solver.dissimilarity_functions
- cassiopeia.tools.autocorrelation
- cassiopeia.tools.branch_length_estimator.IIDExponentialBayesian
- cassiopeia.tools.branch_length_estimator.IIDExponentialMLE
- cassiopeia.tools.coupling
- cassiopeia.tools.parameter_estimators
- cassiopeia.tools.small_parsimony
- cassiopeia.tools.topology
- cassiopeia.tools.tree_metrics