Setup | Data exploration | Full trees | Clone trees | Estimating growth rates | Understanding the function outputs | Downstream analysis | Metadata | Recreating figures | MPN vs. Normal (Fig. 5E) | Single vs. multi-driver (Fig. 5F) | Time from clone initiation to diagnosis (Fig. 5G) | Validation | References / Data sources:

Setup | Simulating trees | Ultrametric trees | Mutation trees | Quantitative comparisons | Max likelihood vs. internal lengths vs. shared mutations | Root Mean Square Error (RMSE) | Mean | Standard deviation | Coverage probability | Varying parameters | Varying n | Varying r (and/or cloneAge) | Varying r or cloneAge? | Performance across r values | References