RidgeRace: ridge regression for continuous ancestral character estimation on phylogenetic trees

Motivation: Ancestral character state reconstruction describes a set of techniques for estimating phenotypic or genetic features of species or related individuals that are the predecessors of those present today. Such reconstructions can reach into the distant past and can provide insights into the...

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Autores principales: Kratsch, Christina, McHardy, Alice C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4147928/
https://www.ncbi.nlm.nih.gov/pubmed/25161243
http://dx.doi.org/10.1093/bioinformatics/btu477
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author Kratsch, Christina
McHardy, Alice C.
author_facet Kratsch, Christina
McHardy, Alice C.
author_sort Kratsch, Christina
collection PubMed
description Motivation: Ancestral character state reconstruction describes a set of techniques for estimating phenotypic or genetic features of species or related individuals that are the predecessors of those present today. Such reconstructions can reach into the distant past and can provide insights into the history of a population or a set of species when fossil data are not available, or they can be used to test evolutionary hypotheses, e.g. on the co-evolution of traits. Typical methods for ancestral character state reconstruction of continuous characters consider the phylogeny of the underlying data and estimate the ancestral process along the branches of the tree. They usually assume a Brownian motion model of character evolution or extensions thereof, requiring specific assumptions on the rate of phenotypic evolution. Results: We suggest using ridge regression to infer rates for each branch of the tree and the ancestral values at each inner node. We performed extensive simulations to evaluate the performance of this method and have shown that the accuracy of its reconstructed ancestral values is competitive to reconstructions using other state-of-the-art software. Using a hierarchical clustering of gene mutation profiles from an ovarian cancer dataset, we demonstrate the use of the method as a feature selection tool. Availability and implementation: The algorithm described here is implemented in C++ as a stand-alone program, and the source code is freely available at http://algbio.cs.uni-duesseldorf.de/software/RidgeRace.tar.gz. Contact: mchardy@hhu.de Supplementary information: Supplementary data are available at Bioinformatics online.
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spelling pubmed-41479282014-09-02 RidgeRace: ridge regression for continuous ancestral character estimation on phylogenetic trees Kratsch, Christina McHardy, Alice C. Bioinformatics Eccb 2014 Proceedings Papers Committee Motivation: Ancestral character state reconstruction describes a set of techniques for estimating phenotypic or genetic features of species or related individuals that are the predecessors of those present today. Such reconstructions can reach into the distant past and can provide insights into the history of a population or a set of species when fossil data are not available, or they can be used to test evolutionary hypotheses, e.g. on the co-evolution of traits. Typical methods for ancestral character state reconstruction of continuous characters consider the phylogeny of the underlying data and estimate the ancestral process along the branches of the tree. They usually assume a Brownian motion model of character evolution or extensions thereof, requiring specific assumptions on the rate of phenotypic evolution. Results: We suggest using ridge regression to infer rates for each branch of the tree and the ancestral values at each inner node. We performed extensive simulations to evaluate the performance of this method and have shown that the accuracy of its reconstructed ancestral values is competitive to reconstructions using other state-of-the-art software. Using a hierarchical clustering of gene mutation profiles from an ovarian cancer dataset, we demonstrate the use of the method as a feature selection tool. Availability and implementation: The algorithm described here is implemented in C++ as a stand-alone program, and the source code is freely available at http://algbio.cs.uni-duesseldorf.de/software/RidgeRace.tar.gz. Contact: mchardy@hhu.de Supplementary information: Supplementary data are available at Bioinformatics online. Oxford University Press 2014-09-01 2014-08-22 /pmc/articles/PMC4147928/ /pubmed/25161243 http://dx.doi.org/10.1093/bioinformatics/btu477 Text en © The Author 2014. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Eccb 2014 Proceedings Papers Committee
Kratsch, Christina
McHardy, Alice C.
RidgeRace: ridge regression for continuous ancestral character estimation on phylogenetic trees
title RidgeRace: ridge regression for continuous ancestral character estimation on phylogenetic trees
title_full RidgeRace: ridge regression for continuous ancestral character estimation on phylogenetic trees
title_fullStr RidgeRace: ridge regression for continuous ancestral character estimation on phylogenetic trees
title_full_unstemmed RidgeRace: ridge regression for continuous ancestral character estimation on phylogenetic trees
title_short RidgeRace: ridge regression for continuous ancestral character estimation on phylogenetic trees
title_sort ridgerace: ridge regression for continuous ancestral character estimation on phylogenetic trees
topic Eccb 2014 Proceedings Papers Committee
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4147928/
https://www.ncbi.nlm.nih.gov/pubmed/25161243
http://dx.doi.org/10.1093/bioinformatics/btu477
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