Accurate reconstruction of insertion-deletion histories by statistical phylogenetics.

The Multiple Sequence Alignment (MSA) is a computational abstraction that represents a partial summary either of indel history, or of structural similarity. Taking the former view (indel history), it is possible to use formal automata theory to generalize the phylogenetic likelihood framework for fi...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Oscar Westesson, Gerton Lunter, Benedict Paten, Ian Holmes
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/3eade5f5b5fa4ed2a190e9ca63d4a7c6
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:3eade5f5b5fa4ed2a190e9ca63d4a7c6
record_format	dspace
spelling	oai:doaj.org-article:3eade5f5b5fa4ed2a190e9ca63d4a7c62021-11-18T07:21:29ZAccurate reconstruction of insertion-deletion histories by statistical phylogenetics.1932-620310.1371/journal.pone.0034572https://doaj.org/article/3eade5f5b5fa4ed2a190e9ca63d4a7c62012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22536326/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203The Multiple Sequence Alignment (MSA) is a computational abstraction that represents a partial summary either of indel history, or of structural similarity. Taking the former view (indel history), it is possible to use formal automata theory to generalize the phylogenetic likelihood framework for finite substitution models (Dayhoff's probability matrices and Felsenstein's pruning algorithm) to arbitrary-length sequences. In this paper, we report results of a simulation-based benchmark of several methods for reconstruction of indel history. The methods tested include a relatively new algorithm for statistical marginalization of MSAs that sums over a stochastically-sampled ensemble of the most probable evolutionary histories. For mammalian evolutionary parameters on several different trees, the single most likely history sampled by our algorithm appears less biased than histories reconstructed by other MSA methods. The algorithm can also be used for alignment-free inference, where the MSA is explicitly summed out of the analysis. As an illustration of our method, we discuss reconstruction of the evolutionary histories of human protein-coding genes.Oscar WestessonGerton LunterBenedict PatenIan HolmesPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 4, p e34572 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Oscar Westesson Gerton Lunter Benedict Paten Ian Holmes Accurate reconstruction of insertion-deletion histories by statistical phylogenetics.
description	The Multiple Sequence Alignment (MSA) is a computational abstraction that represents a partial summary either of indel history, or of structural similarity. Taking the former view (indel history), it is possible to use formal automata theory to generalize the phylogenetic likelihood framework for finite substitution models (Dayhoff's probability matrices and Felsenstein's pruning algorithm) to arbitrary-length sequences. In this paper, we report results of a simulation-based benchmark of several methods for reconstruction of indel history. The methods tested include a relatively new algorithm for statistical marginalization of MSAs that sums over a stochastically-sampled ensemble of the most probable evolutionary histories. For mammalian evolutionary parameters on several different trees, the single most likely history sampled by our algorithm appears less biased than histories reconstructed by other MSA methods. The algorithm can also be used for alignment-free inference, where the MSA is explicitly summed out of the analysis. As an illustration of our method, we discuss reconstruction of the evolutionary histories of human protein-coding genes.
format	article
author	Oscar Westesson Gerton Lunter Benedict Paten Ian Holmes
author_facet	Oscar Westesson Gerton Lunter Benedict Paten Ian Holmes
author_sort	Oscar Westesson
title	Accurate reconstruction of insertion-deletion histories by statistical phylogenetics.
title_short	Accurate reconstruction of insertion-deletion histories by statistical phylogenetics.
title_full	Accurate reconstruction of insertion-deletion histories by statistical phylogenetics.
title_fullStr	Accurate reconstruction of insertion-deletion histories by statistical phylogenetics.
title_full_unstemmed	Accurate reconstruction of insertion-deletion histories by statistical phylogenetics.
title_sort	accurate reconstruction of insertion-deletion histories by statistical phylogenetics.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/3eade5f5b5fa4ed2a190e9ca63d4a7c6
work_keys_str_mv	AT oscarwestesson accuratereconstructionofinsertiondeletionhistoriesbystatisticalphylogenetics AT gertonlunter accuratereconstructionofinsertiondeletionhistoriesbystatisticalphylogenetics AT benedictpaten accuratereconstructionofinsertiondeletionhistoriesbystatisticalphylogenetics AT ianholmes accuratereconstructionofinsertiondeletionhistoriesbystatisticalphylogenetics
_version_	1718423591587938304

Accurate reconstruction of insertion-deletion histories by statistical phylogenetics.

Ejemplares similares