ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search

Illustration of cell lineage tree, genotypes with uncertainty, and input of ScisTree2. (A) The true cell lineage tree with five cells and six sites (with mutations labeling branches). Infinite-sites model: one mutation per site. Four internal nodes: a to d. (B) The true (binary) genotypes. There are five cells and six SNV sites. (C) The input of ScisTree2 is the genotype probability matrix of genotypes being the wild type (0). The two boldfaced positions denote genotypes, called using the maximum probability allele, that do not agree with the true genotypes. For example, for the cell C₃ and the site S₆, M[3, 6] = 0.7, which would wrongly call this genotype the wild type (0).