方法对比

	单细胞系统发育分析	系统发育分析
领域	生物信息学	生物信息学
方法族	Process / pipeline	Process / pipeline
起源年份	2014-2020 (rapid development period)	1960s-1981 (distance trees ~1967; ML framework formalised 1981)
提出者	Multiple groups; foundational tools: Trapnell et al. (Monocle, 2014), Jones et al. (Cassiopeia, 2020)	Joseph Felsenstein (maximum likelihood framework); Walter Fitch and Emanuel Margoliash (distance methods)
类型	Computational phylogenetic inference pipeline	Computational inference method
开创性文献	Jones, M. G., Khodaverdian, A., Quinn, J. J., Chan, M. M., Hussmann, J. A., Wang, R., Xu, C., Weissman, J. S., & Yosef, N. (2020). Inference of single-cell phylogenies from lineage tracing data using Cassiopeia. Genome Biology, 21(1), 92.	Felsenstein, J. (2004). Inferring Phylogenies. Sinauer Associates. ISBN: 978-0878931774
别名	scPhylogeny, single-cell lineage tracing, clonal phylogenetics, single-cell tree inference	molecular phylogenetics, phylogenetic inference, evolutionary tree reconstruction, phylogenomics
相关	4	5
摘要	Single-cell phylogenetic analysis reconstructs evolutionary or developmental trees from single-cell sequencing data, tracing how individual cells diverged from a common ancestor. By leveraging somatic mutations, CRISPR-introduced barcodes, or copy-number changes as heritable characters, this method maps clonal relationships within tumors, developing tissues, or immune repertoires with unprecedented cellular resolution.	Phylogenetic analysis reconstructs the evolutionary history of organisms, genes, or proteins by comparing molecular sequence data and estimating the branching tree that best explains observed similarities and differences. Rooted in the work of Felsenstein and colleagues from the 1960s onward, it is a cornerstone technique in evolutionary biology, microbiology, epidemiology, and comparative genomics, supporting tasks from tracing viral outbreak origins to classifying novel species.