突变谱在分子进化中的公认重要性尚未在人类癌症研究和模型生物之外得到充分利用。 GenBank 存储库中丰富的种内多态性数据涵盖了广泛的基因和物种，为详细的突变谱分析提供了尚未开发的机会。现有方法的不足之处在于忽略了系统发育树内部分支上的中间替换，并且缺乏跨物种突变比较的能力。为了应对这些挑战，我们推出了 NeMu pipeline（可在 https://nemu-pipeline.com 上获取），这是一种基于系统发生原理的工具，旨在提供全面且可扩展的突变谱分析。 NeMu 利用来自众多可用基因组项目的大量序列数据，快速准确地重建中性突变谱。该工具有助于重建基因和物种特异性突变谱，有助于更深入地了解已知物种的广泛进化机制。© 作者 2024。由牛津大学出版社代表 Nucleic Acids 出版研究。

The recognized importance of mutational spectra in molecular evolution is yet to be fully exploited beyond human cancer studies and model organisms. The wealth of intraspecific polymorphism data in the GenBank repository, covering a broad spectrum of genes and species, presents an untapped opportunity for detailed mutational spectrum analysis. Existing methods fall short by ignoring intermediate substitutions on the inner branches of phylogenetic trees and lacking the capability for cross-species mutational comparisons. To address these challenges, we present the NeMu pipeline, available at https://nemu-pipeline.com, a tool grounded in phylogenetic principles designed to provide comprehensive and scalable analysis of mutational spectra. Utilizing extensive sequence data from numerous available genome projects, NeMu rapidly and accurately reconstructs the neutral mutational spectrum. This tool, facilitating the reconstruction of gene- and species-specific mutational spectra, contributes to a deeper understanding of evolutionary mechanisms across the broad spectrum of known species.© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.