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Fig. 4 | Genome Biology

Fig. 4

From: Inference of single-cell phylogenies from lineage tracing data using Cassiopeia

Fig. 4

Cassiopeia can reconstruct high-resolution phylogenetic trees from empirical lineage tracing data. The full phylogenetic tree for Clone 3 (a), consisting of 7289 cells, was reconstructed using Cassiopeia-Hybrid (with priors) and is displayed. The phylogram represents cell-cell relationships, and each cell is colored by sample ID at the first split (plate 0 or 1). The character matrix is displayed with each unique character state (or “indel”) represented by distinct colors (light gray represents uncut sites; white represents missing values). Of these 7289 cells, 96% were uniquely tagged by their character states. b, c Nested, expanded views of the phylogram and character matrices. As expected, Cassiopeia correctly relates cells with similar character states, and closely related cells are found within the same culture plate. d A histogram of the tree depth of each leaf from the root (mean = 8.22, max = 15). e Concordance between normalized allelic distance and normalized phylogenetic distance (see the “Methods” section; Pearson’s correlation = 0.53)

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