方法对比

	基于网络的系统发育分析	多组学系统发育分析
领域	生物信息学	生物信息学
方法族	Process / pipeline	Process / pipeline
起源年份	1992–2004 (foundational algorithms); broader development 1990s–2010s	Late 1990s–2000s (genome-scale; multi-omics integration ~2010s)
提出者	Hans-Jürgen Bandelt & Andreas Dress (split decomposition); David Bryant & Vincent Moulton (Neighbor-Net)	Hedges, Kumar, Philippe and colleagues (phylogenomics pioneers, late 1990s–2000s)
类型	Computational phylogenetic method	Computational phylogenetic inference pipeline
开创性文献	Bandelt, H.-J., & Dress, A. W. M. (1992). Split decomposition: A new and useful approach to phylogenetic analysis of distance data. Molecular Phylogenetics and Evolution, 1(3), 242–252.	Delsuc, F., Brinkmann, H., & Philippe, H. (2005). Phylogenomics and the reconstruction of the tree of life. Nature Reviews Genetics, 6(5), 361–375.
别名	phylogenetic network, reticulate phylogenetics, split network analysis, evolutionary network inference	phylogenomics, multi-omic phylogenetics, integrative phylogenomics, omics-based phylogenetics
相关	6	0
摘要	Network-based phylogenetic analysis constructs graph-structured representations of evolutionary relationships that explicitly accommodate reticulate events — including hybridization, horizontal gene transfer, recombination, and incomplete lineage sorting — which strictly bifurcating phylogenetic trees cannot represent. Instead of forcing sequences into a single bifurcating tree, the method infers splits or reticulations in the data and visualises them as a network, revealing conflicting phylogenetic signals that are biologically informative.	Multi-omics phylogenetic analysis reconstructs evolutionary relationships among organisms by integrating sequence data from multiple molecular layers — genomes, transcriptomes, and proteomes — rather than relying on a single marker gene. By combining thousands of orthologous loci across omics layers, the approach dramatically reduces stochastic error, resolves ancient divergences that single-gene trees cannot, and yields a far more robust and well-supported topology of the tree of life or a focal clade.