Simulator¶
Our simulators for cassiopeia are split up into those that simulate topologies and those that simulate data on top of the topologies.
Tree Simulators¶
We have several frameworks available for simulating topologies:
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Simulator class for a general forward birth-death process with fitness. |
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Simulate a complete binary tree. |
Simulates a clonal population which develops one fit subclone. |
Data Simulators¶
These simulators are subclasses of the DataSimulator class and implement the overlay_data method which simulates data according to a given topology.
Simulates Cas9-based lineage tracing data. |
Leaf SubSamplers¶
These are utilities for subsampling lineages for benchmarking purposes. For example, sampling a random proportion of leaves or grouping together cells into clades to model spatial data.
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