系统发育网络的分析优化。

IF 3.9 2区 生物学 Q1 EVOLUTIONARY BIOLOGY Cladistics Pub Date : 2023-07-19 DOI:10.1111/cla.12552
Ward C. Wheeler, Alexander J. Washburn
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引用次数: 1

摘要

描述了一种用于在软连线系统发育网络上优化特征数据(例如定性核酸序列)的算法。这里提出的算法是在简约准则下为树开发的算法的扩展,可以形成系统发育网络搜索程序的基础。尽管这个问题(通常)是NP难优化,但我们在这里描述的基于分辨率的算法利用了包含网络边缘的子图中大量的共享结构,减少了执行时间,并允许对经验数据集进行分析。
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Parsimony optimization of phylogenetic networks

An algorithm is described for the optimization of character data (e.g. qualitative, nucleic acid sequence) on softwired phylogenetic networks. The algorithm presented here is an extension of those developed for trees under the parsimony criterion and can form the basis for phylogenetic network search procedures. Although the problem is (in general) an NP-Hard optimization, the resolution-based algorithm we describe here capitalizes on the significant amount of shared structure in sub-graphs containing network edges, reducing the execution time and allowing for the analysis of empirical datasets.

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来源期刊
Cladistics
Cladistics 生物-进化生物学
CiteScore
8.60
自引率
5.60%
发文量
34
期刊介绍: Cladistics publishes high quality research papers on systematics, encouraging debate on all aspects of the field, from philosophy, theory and methodology to empirical studies and applications in biogeography, coevolution, conservation biology, ontogeny, genomics and paleontology. Cladistics is read by scientists working in the research fields of evolution, systematics and integrative biology and enjoys a consistently high position in the ISI® rankings for evolutionary biology.
期刊最新文献
Revisiting the backbone phylogeny and inferring the evolutionary trends in inflorescence of Elsholtzieae (Lamiaceae): new insights from orthologous nuclear genes. "Dark taxonomy": A new protocol for overcoming the taxonomic impediments for dark taxa and broadening the taxon base for biodiversity assessment. Phylogenetic minimum description length: an optimality criterion based on algorithmic complexity. Issue Information Accuracy of phylogenetic reconstructions from continuous characters analysed under parsimony and its parametric correlates.
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