Probabilistic phylogenetic inference with insertions and deletions.

A fundamental task in sequence analysis is to calculate the probability of a multiple alignment given a phylogenetic tree relating the sequences and an evolutionary model describing how sequences change over time. However, the most widely used phylogenetic models only account for residue substitutio...

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Autores principales:	Elena Rivas, Sean R Eddy
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2008
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/8cdc1c8ba6384fb0a5f929484262df74
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spelling	oai:doaj.org-article:8cdc1c8ba6384fb0a5f929484262df742021-11-25T05:41:59ZProbabilistic phylogenetic inference with insertions and deletions.1553-734X1553-735810.1371/journal.pcbi.1000172https://doaj.org/article/8cdc1c8ba6384fb0a5f929484262df742008-09-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18787703/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358A fundamental task in sequence analysis is to calculate the probability of a multiple alignment given a phylogenetic tree relating the sequences and an evolutionary model describing how sequences change over time. However, the most widely used phylogenetic models only account for residue substitution events. We describe a probabilistic model of a multiple sequence alignment that accounts for insertion and deletion events in addition to substitutions, given a phylogenetic tree, using a rate matrix augmented by the gap character. Starting from a continuous Markov process, we construct a non-reversible generative (birth-death) evolutionary model for insertions and deletions. The model assumes that insertion and deletion events occur one residue at a time. We apply this model to phylogenetic tree inference by extending the program dnaml in phylip. Using standard benchmarking methods on simulated data and a new "concordance test" benchmark on real ribosomal RNA alignments, we show that the extended program dnamlepsilon improves accuracy relative to the usual approach of ignoring gaps, while retaining the computational efficiency of the Felsenstein peeling algorithm.Elena RivasSean R EddyPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 4, Iss 9, p e1000172 (2008)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Elena Rivas Sean R Eddy Probabilistic phylogenetic inference with insertions and deletions.
description	A fundamental task in sequence analysis is to calculate the probability of a multiple alignment given a phylogenetic tree relating the sequences and an evolutionary model describing how sequences change over time. However, the most widely used phylogenetic models only account for residue substitution events. We describe a probabilistic model of a multiple sequence alignment that accounts for insertion and deletion events in addition to substitutions, given a phylogenetic tree, using a rate matrix augmented by the gap character. Starting from a continuous Markov process, we construct a non-reversible generative (birth-death) evolutionary model for insertions and deletions. The model assumes that insertion and deletion events occur one residue at a time. We apply this model to phylogenetic tree inference by extending the program dnaml in phylip. Using standard benchmarking methods on simulated data and a new "concordance test" benchmark on real ribosomal RNA alignments, we show that the extended program dnamlepsilon improves accuracy relative to the usual approach of ignoring gaps, while retaining the computational efficiency of the Felsenstein peeling algorithm.
format	article
author	Elena Rivas Sean R Eddy
author_facet	Elena Rivas Sean R Eddy
author_sort	Elena Rivas
title	Probabilistic phylogenetic inference with insertions and deletions.
title_short	Probabilistic phylogenetic inference with insertions and deletions.
title_full	Probabilistic phylogenetic inference with insertions and deletions.
title_fullStr	Probabilistic phylogenetic inference with insertions and deletions.
title_full_unstemmed	Probabilistic phylogenetic inference with insertions and deletions.
title_sort	probabilistic phylogenetic inference with insertions and deletions.
publisher	Public Library of Science (PLoS)
publishDate	2008
url	https://doaj.org/article/8cdc1c8ba6384fb0a5f929484262df74
work_keys_str_mv	AT elenarivas probabilisticphylogeneticinferencewithinsertionsanddeletions AT seanreddy probabilisticphylogeneticinferencewithinsertionsanddeletions
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Probabilistic phylogenetic inference with insertions and deletions.

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