Cargando…

Assessing the Applicability of the GTR Nucleotide Substitution Model Through Simulations

The General Time Reversible (GTR) model of nucleotide substitution is at the core of many distance-based and character-based phylogeny inference methods. The procedure described by Waddell and Steel (1997), for estimating distances and instantaneous substitution rate matrices, R, under the GTR model...

Descripción completa

Detalles Bibliográficos
Autores principales: Gatto, Laurent, Catanzaro, Daniele, Milinkovitch, Michel C.
Formato: Texto
Lenguaje:English
Publicado: Libertas Academica 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674669/
https://www.ncbi.nlm.nih.gov/pubmed/19455208
_version_ 1782166662746734592
author Gatto, Laurent
Catanzaro, Daniele
Milinkovitch, Michel C.
author_facet Gatto, Laurent
Catanzaro, Daniele
Milinkovitch, Michel C.
author_sort Gatto, Laurent
collection PubMed
description The General Time Reversible (GTR) model of nucleotide substitution is at the core of many distance-based and character-based phylogeny inference methods. The procedure described by Waddell and Steel (1997), for estimating distances and instantaneous substitution rate matrices, R, under the GTR model, is known to be inapplicable under some conditions, ie, it leads to the inapplicability of the GTR model. Here, we simulate the evolution of DNA sequences along 12 trees characterized by different combinations of tree length, (non-)homogeneity of the substitution rate matrix R, and sequence length. We then evaluate both the frequency of the GTR model inapplicability for estimating distances and the accuracy of inferred alignments. Our results indicate that, inapplicability of the Waddel and Steel’s procedure can be considered a real practical issue, and illustrate that the probability of this inapplicability is a function of substitution rates and sequence length. We also discuss the implications of our results on the current implementations of maximum likelihood and Bayesian methods.
format Text
id pubmed-2674669
institution National Center for Biotechnology Information
language English
publishDate 2007
publisher Libertas Academica
record_format MEDLINE/PubMed
spelling pubmed-26746692009-05-19 Assessing the Applicability of the GTR Nucleotide Substitution Model Through Simulations Gatto, Laurent Catanzaro, Daniele Milinkovitch, Michel C. Evol Bioinform Online Original Research The General Time Reversible (GTR) model of nucleotide substitution is at the core of many distance-based and character-based phylogeny inference methods. The procedure described by Waddell and Steel (1997), for estimating distances and instantaneous substitution rate matrices, R, under the GTR model, is known to be inapplicable under some conditions, ie, it leads to the inapplicability of the GTR model. Here, we simulate the evolution of DNA sequences along 12 trees characterized by different combinations of tree length, (non-)homogeneity of the substitution rate matrix R, and sequence length. We then evaluate both the frequency of the GTR model inapplicability for estimating distances and the accuracy of inferred alignments. Our results indicate that, inapplicability of the Waddel and Steel’s procedure can be considered a real practical issue, and illustrate that the probability of this inapplicability is a function of substitution rates and sequence length. We also discuss the implications of our results on the current implementations of maximum likelihood and Bayesian methods. Libertas Academica 2007-02-04 /pmc/articles/PMC2674669/ /pubmed/19455208 Text en Copyright © 2006 The authors. http://creativecommons.org/licenses/by/3.0 This article is published under the Creative Commons Attribution By licence. For further information go to: http://creativecommons.org/licenses/by/3.0. (http://creativecommons.org/licenses/by/3.0)
spellingShingle Original Research
Gatto, Laurent
Catanzaro, Daniele
Milinkovitch, Michel C.
Assessing the Applicability of the GTR Nucleotide Substitution Model Through Simulations
title Assessing the Applicability of the GTR Nucleotide Substitution Model Through Simulations
title_full Assessing the Applicability of the GTR Nucleotide Substitution Model Through Simulations
title_fullStr Assessing the Applicability of the GTR Nucleotide Substitution Model Through Simulations
title_full_unstemmed Assessing the Applicability of the GTR Nucleotide Substitution Model Through Simulations
title_short Assessing the Applicability of the GTR Nucleotide Substitution Model Through Simulations
title_sort assessing the applicability of the gtr nucleotide substitution model through simulations
topic Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674669/
https://www.ncbi.nlm.nih.gov/pubmed/19455208
work_keys_str_mv AT gattolaurent assessingtheapplicabilityofthegtrnucleotidesubstitutionmodelthroughsimulations
AT catanzarodaniele assessingtheapplicabilityofthegtrnucleotidesubstitutionmodelthroughsimulations
AT milinkovitchmichelc assessingtheapplicabilityofthegtrnucleotidesubstitutionmodelthroughsimulations