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

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Publication Date: 29 Sep 2011

Type: Original Research

Journal: Evolutionary Bioinformatics

Citation: Evolutionary Bioinformatics 2011:7 159-170

doi: 10.4137/EBO.S7182

Abstract

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.


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