A new support measure to quantify the impact of local optima in phylogenetic analyses.

Grant Brammer, Seung-Jin Sul, Tiffani L Williams

Research output: Contribution to journalArticlepeer-review


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.
Original languageEnglish (US)
Pages (from-to)EBO.S7182
JournalEvolutionary Bioinformatics
Issue number7
StatePublished - Sep 29 2011
Externally publishedYes

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledged KAUST grant number(s): KUS-C1-016-04
Acknowledgements: This work was supported by the National Science Foundation under grants DEB-0629849, IIS-0713618, and IIS-1018785.We would like to thank Matthew Gitzendanner, Paul Lewis, and David Soltis for providing us with the tree collections used in this paper. Moreover, this publication is based in part on work supported by Award No. KUS-C1-016-04, made by King Abdullah University of Science and Technology (KAUST).
This publication acknowledges KAUST support, but has no KAUST affiliated authors.


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