A New Support Measure to Quantify the Impact of Local Optima in Phylogenetic Analyses

Evolutionary Bioinformatics

Grant Brammer¹ 

关键词: phylogenetic;    support measure;    visualization;   

DOI  :  10.4137/EBO.S7182

学科分类：生物技术

来源: Sage Journals

【 摘 要 】

Phylogentic analyses are often incorrectly assumed to have stabilized to a single optimum. However, a set of trees from a phylogenetic analysis may contain multiple distinct local optima with each optimum providing different levels of support for each clade. For situations with multiple local optima, we propose p-support which is a clade support measure that shows the impact optima have on a final consensus tree. Our p-support measure is implemented in our PeakMapper software package. We study our approach on two published, large-scale biological tree collections. PeakMapper shows that each data set contains multiple local optima, p-support shows that both datasets contain clades in the majority consensus tree that are only supported by a subset of the local optima. Clades with low p-support are most likely to benefit from further investigation. These tools provide researchers with new information regarding phylogenetic analyses beyond what is provided by other support measures alone.

【 授权许可】

Unknown