Fig. 1

The J-SPACE framework. Schematic representation of J-SPACE. A First, the algorithm simulates the spatial growth of the cells over an arbitrary graph. Then, J-SPACE simulates a spatial sampling (black circle) at a given time point. B J-SPACE reconstructs the phylogeny of the sampled cells (i.e., the leaves of the tree) and, given an ancestral genome, it generates the ground-truth sequence of the sampled cells using various substitution models. C A NGS experiment is simulated to return synthetic reads as outputs