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EREM: Parameter Estimation and Ancestral Reconstruction by Expectation-Maximization Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution

Evolutionary binary characters are features of species or genes, indicating the absence (value zero) or presence (value one) of some property. Examples include eukaryotic gene architecture (the presence or absence of an intron in a particular locus), gene content, and morphological characters. In ma...

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Detalles Bibliográficos
Autores principales: Carmel, Liran, Wolf, Yuri I., Rogozin, Igor B., Koonin, Eugene V.
Formato: Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2866244/
https://www.ncbi.nlm.nih.gov/pubmed/20467467
http://dx.doi.org/10.1155/2010/167408
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author Carmel, Liran
Wolf, Yuri I.
Rogozin, Igor B.
Koonin, Eugene V.
author_facet Carmel, Liran
Wolf, Yuri I.
Rogozin, Igor B.
Koonin, Eugene V.
author_sort Carmel, Liran
collection PubMed
description Evolutionary binary characters are features of species or genes, indicating the absence (value zero) or presence (value one) of some property. Examples include eukaryotic gene architecture (the presence or absence of an intron in a particular locus), gene content, and morphological characters. In many studies, the acquisition of such binary characters is assumed to represent a rare evolutionary event, and consequently, their evolution is analyzed using various flavors of parsimony. However, when gain and loss of the character are not rare enough, a probabilistic analysis becomes essential. Here, we present a comprehensive probabilistic model to describe the evolution of binary characters on a bifurcating phylogenetic tree. A fast software tool, EREM, is provided, using maximum likelihood to estimate the parameters of the model and to reconstruct ancestral states (presence and absence in internal nodes) and events (gain and loss events along branches).
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spelling pubmed-28662442010-05-13 EREM: Parameter Estimation and Ancestral Reconstruction by Expectation-Maximization Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution Carmel, Liran Wolf, Yuri I. Rogozin, Igor B. Koonin, Eugene V. Adv Bioinformatics Resource Review Evolutionary binary characters are features of species or genes, indicating the absence (value zero) or presence (value one) of some property. Examples include eukaryotic gene architecture (the presence or absence of an intron in a particular locus), gene content, and morphological characters. In many studies, the acquisition of such binary characters is assumed to represent a rare evolutionary event, and consequently, their evolution is analyzed using various flavors of parsimony. However, when gain and loss of the character are not rare enough, a probabilistic analysis becomes essential. Here, we present a comprehensive probabilistic model to describe the evolution of binary characters on a bifurcating phylogenetic tree. A fast software tool, EREM, is provided, using maximum likelihood to estimate the parameters of the model and to reconstruct ancestral states (presence and absence in internal nodes) and events (gain and loss events along branches). Hindawi Publishing Corporation 2010 2010-05-06 /pmc/articles/PMC2866244/ /pubmed/20467467 http://dx.doi.org/10.1155/2010/167408 Text en Copyright © 2010 Liran Carmel et al. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Resource Review
Carmel, Liran
Wolf, Yuri I.
Rogozin, Igor B.
Koonin, Eugene V.
EREM: Parameter Estimation and Ancestral Reconstruction by Expectation-Maximization Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution
title EREM: Parameter Estimation and Ancestral Reconstruction by Expectation-Maximization Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution
title_full EREM: Parameter Estimation and Ancestral Reconstruction by Expectation-Maximization Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution
title_fullStr EREM: Parameter Estimation and Ancestral Reconstruction by Expectation-Maximization Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution
title_full_unstemmed EREM: Parameter Estimation and Ancestral Reconstruction by Expectation-Maximization Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution
title_short EREM: Parameter Estimation and Ancestral Reconstruction by Expectation-Maximization Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution
title_sort erem: parameter estimation and ancestral reconstruction by expectation-maximization algorithm for a probabilistic model of genomic binary characters evolution
topic Resource Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2866244/
https://www.ncbi.nlm.nih.gov/pubmed/20467467
http://dx.doi.org/10.1155/2010/167408
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