Data and code from: TiDeTree: A Bayesian phylogenetic framework to estimate single-cell trees and population dynamic parameters from genetic lineage tracing data

The development of organisms and tissues is dictated by an elaborate balance between cell division, apoptosis and differentiation: the cell population dynamics. To quantify these dynamics, we propose a phylodynamic inference approach based on data from single-cell lineage recorders. For this purpose, we developed a Bayesian phylogenetic framework, TiDeTree, that uses lineage recorder data as input to estimate time-scaled single-cell trees. By implementing TiDeTree in the BEAST 2 platform, we enable joint inference of the time-scaled trees and, for the first time, the cell population dynamics. We validated TiDeTree using simulations and showed that its performance can further be improved by including multiple sources of additional independent information into the inference, such as frequencies of editing outcomes or experimental replicates. We benchmarked TiDeTree against state-of-the-art methods and show that it performs comparably in terms of tree topology estimation and additionally e..., , , , # Data and code from: TiDeTree: A Bayesian phylogenetic framework to estimate single-cell trees and population dynamic parameters from genetic lineage tracing data

Analyses and figures associated with the manuscript (https://doi.org/10.1098/rspb.2022.1844).

## Description of data

The development of a multicellular organism is governed by an elaborate balance between cell division, death, and differentiation. These core developmental processes can be quantified from single-cell phylogenies. Here we present TiDeTree, a Bayesian phylogenetic framework for inference of time-scaled single-cell phylogenies and population dynamic parameters such as cell division, death, and differentiation rates from genetic lineage tracing data. We show that the performance of TiDeTree can be improved by incorporating multiple sources of additional independent information into the inference. Finally, we apply TiDeTree to a lineage tracing dataset to estimate time-scaled phylogenies, cell division, and apop...,