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. 2023 Feb 22;14:982. doi: 10.1038/s41467-023-36202-y

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a Schematic diagram describing the bulk DNA-seq and scRNA-seq data input. The output of PhylEx includes the tree and assignment of SNVs and cells to clones. b The cherry shaped tree used in the illustrative example for identifying branching structure from scRNA-seq. The true values of the cellular prevalences are indicated for each clone. c Inferred tree and cellular prevalences from integrated analysis of bulk DNA-seq and scRNA-seq. d Inferred tree and cellular prevalences using bulk DNA-seq. e The heatmap of the variant read counts of single-cells across loci and f. the heatmap of the variant read counts of single cells after co-clustering of cells and SNVs using PhylEx. All the cells share common set of ancestral SNVs and we can see two clusters of cells based on their clonal membership. Source data for e, f are provided as a Source Data file.