Figure 1.

TedSim workflow. The cell state tree models the true trajectories of cell differentiation and the cell division tree represents the true lineage. When traversing the cell division tree from root to leaves, the cell states are determined based on the state tree and the asymmetric division events (denoted by red edges in the cell division tree). TedSim simultaneously simulates gene expressions and lineage barcodes of all the cells, while the state and lineage relationships of the cells are maintained. The simulated data can be used to test not only TI or tree reconstruction methods, but also hybrid methods that use both gene expression and lineage barcode data.