Fig. 6
a Input data from single-nucleus sequencing of 32 cells from a triple-negative breast cancer [34]. As the rate of missing values in the original data was around 1%, the authors set all missing data points equal to 0; in the dataset, allelic dropout is equal to 9.73×10−2, and false discovery equal to 1.24×10−6. b Phylogenetic tree manually curated in [34]. Mutations are annotated to the trunk if they are ubiquitous across cells and a bulk control sample. Subclonal mutations appearing only in more than one cell. c. Mutational graph obtained with Edmonds algorithm; p-values are obtained by 3 tests for conditions (Eq. 1) and overlap (hypergeometric test), and edges annotated with a posteriori non-parametric bootstrap scores (100 estimates). For these data, all TRaIT’s algorithms return trees (Additional file 1: Figure S17-18), consistently with the manually curated phylogeny (A). Most edges are highly confident (p<0.05), except for groups of variables with the same frequency which have unknown ordering (red edges). The ordering of mutations in subclones A1, A2 and tumour initiation has high bootstrap estimates (>75%). Yellow circles mark the edges retrieved also by SCITE. d. We also performed clonal tree inference with OncoNEM, which predicts 10 clones. Mutations are assigned to clones via maximum a posteriori estimates. The mutational orderings of the early clonal expansion of the tumour and of most of the late subclonal events are consistent with TRaIT’s prediction