Extended Data Fig. 7: Performance of tree-building algorithms used on embryonic data.

a, Table summarizing contemporary Cas9-based lineage tracers that have been applied to vertebrate development, highlighting attributes that differ between the studies. See Supplementary Methods for a more detailed overview of key characteristics of our technology. Single asterisk denotes that the study reports the average fraction recovered by tissue for integrations that cannot be distinguished, such that percentages reported here are effectively equivalent to our ‘≥1 intBC’ metric. Double asterisk indicates that the value refers to a plate-based DNA-sequencing approach that can be applied to all methods to improve target-site recovery. Triple asterisk denotes a range of cells in which at least one intBC is confidently detected and scored. Quadruple asterisk denotes that the study presents a tree reconstruction method, but includes results that predominantly rely on clonal analysis. b, Table of allele complexity, number of nodes and log-likelihood scores for embryos. Tree likelihoods are calculated using indel frequencies estimated from all embryo data (Fig. 2c, Extended Data Fig. 4, Supplementary Methods). Bold scores indicate the reconstruction algorithm selected for each embryo (trees shown in Fig. 4, Extended Data Figs. 8, 9). c, log-likelihood of trees generated using either the greedy or biased sampling approach as a function of complexity, which is measured as the number of unique alleles. There is near-equivalent performance of the two algorithms for low-complexity embryos, but the greedy algorithm produces higher-likelihood trees for embryos with larger numbers of unique alleles.