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

Handle URI:
http://hdl.handle.net/10754/596759
Title:
A new support measure to quantify the impact of local optima in phylogenetic analyses.
Authors:
Brammer, Grant; Sul, Seung-Jin; Williams, Tiffani L
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.
Citation:
Brammer, Seung-Jin Sul, Tiffani L. Williams (2011) A New Support Measure to Quantify the Impact of Local Optima in Phylogenetic Analyses. EBO: 159. Available: http://dx.doi.org/10.4137/EBO.S7182.
Publisher:
Libertas Academica, Ltd.
Journal:
Evolutionary Bioinformatics
KAUST Grant Number:
KUS-C1-016-04
Issue Date:
29-Sep-2011
DOI:
10.4137/EBO.S7182
PubMed ID:
22065522
PubMed Central ID:
PMC3204936
Type:
Article
ISSN:
1176-9343
Sponsors:
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).
Appears in Collections:
Publications Acknowledging KAUST Support

Full metadata record

DC FieldValue Language
dc.contributor.authorBrammer, Granten
dc.contributor.authorSul, Seung-Jinen
dc.contributor.authorWilliams, Tiffani Len
dc.date.accessioned2016-02-21T08:50:04Zen
dc.date.available2016-02-21T08:50:04Zen
dc.date.issued2011-09-29en
dc.identifier.citationBrammer, Seung-Jin Sul, Tiffani L. Williams (2011) A New Support Measure to Quantify the Impact of Local Optima in Phylogenetic Analyses. EBO: 159. Available: http://dx.doi.org/10.4137/EBO.S7182.en
dc.identifier.issn1176-9343en
dc.identifier.pmid22065522en
dc.identifier.doi10.4137/EBO.S7182en
dc.identifier.urihttp://hdl.handle.net/10754/596759en
dc.description.abstractPhylogentic 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.en
dc.description.sponsorshipThis 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).en
dc.publisherLibertas Academica, Ltd.en
dc.rightsThis is an open access article. Unrestricted non-commercial use is permitted provided the original work is properly cited.en
dc.subjectPhylogeneticen
dc.subjectVisualizationen
dc.subjectSupport Measureen
dc.titleA new support measure to quantify the impact of local optima in phylogenetic analyses.en
dc.typeArticleen
dc.identifier.journalEvolutionary Bioinformaticsen
dc.identifier.pmcidPMC3204936en
dc.contributor.institutionTexas A and M University, College Station, United Statesen
dc.contributor.institutionJ. Craig Venter Institute, Rockville, United Statesen
kaust.grant.numberKUS-C1-016-04en

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