Treelength optimization for phylogeny estimation.

The standard approach to phylogeny estimation uses two phases, in which the first phase produces an alignment on a set of homologous sequences, and the second phase estimates a tree on the multiple sequence alignment. POY, a method which seeks a tree/alignment pair minimizing the total treelength, i...

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Autores principales:	Kevin Liu, Tandy Warnow
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/2241f0f1ee33409a80a95f556451fd22
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spelling	oai:doaj.org-article:2241f0f1ee33409a80a95f556451fd222021-11-18T07:24:46ZTreelength optimization for phylogeny estimation.1932-620310.1371/journal.pone.0033104https://doaj.org/article/2241f0f1ee33409a80a95f556451fd222012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22442677/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203The standard approach to phylogeny estimation uses two phases, in which the first phase produces an alignment on a set of homologous sequences, and the second phase estimates a tree on the multiple sequence alignment. POY, a method which seeks a tree/alignment pair minimizing the total treelength, is the most widely used alternative to this two-phase approach. The topological accuracy of trees computed under treelength optimization is, however, controversial. In particular, one study showed that treelength optimization using simple gap penalties produced poor trees and alignments, and suggested the possibility that if POY were used with an affine gap penalty, it might be able to be competitive with the best two-phase methods. In this paper we report on a study addressing this possibility. We present a new heuristic for treelength, called BeeTLe (Better Treelength), that is guaranteed to produce trees at least as short as POY. We then use this heuristic to analyze a large number of simulated and biological datasets, and compare the resultant trees and alignments to those produced using POY and also maximum likelihood (ML) and maximum parsimony (MP) trees computed on a number of alignments. In general, we find that trees produced by BeeTLe are shorter and more topologically accurate than POY trees, but that neither POY nor BeeTLe produces trees as topologically accurate as ML trees produced on standard alignments. These findings, taken as a whole, suggest that treelength optimization is not as good an approach to phylogenetic tree estimation as maximum likelihood based upon good alignment methods.Kevin LiuTandy WarnowPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 3, p e33104 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Kevin Liu Tandy Warnow Treelength optimization for phylogeny estimation.
description	The standard approach to phylogeny estimation uses two phases, in which the first phase produces an alignment on a set of homologous sequences, and the second phase estimates a tree on the multiple sequence alignment. POY, a method which seeks a tree/alignment pair minimizing the total treelength, is the most widely used alternative to this two-phase approach. The topological accuracy of trees computed under treelength optimization is, however, controversial. In particular, one study showed that treelength optimization using simple gap penalties produced poor trees and alignments, and suggested the possibility that if POY were used with an affine gap penalty, it might be able to be competitive with the best two-phase methods. In this paper we report on a study addressing this possibility. We present a new heuristic for treelength, called BeeTLe (Better Treelength), that is guaranteed to produce trees at least as short as POY. We then use this heuristic to analyze a large number of simulated and biological datasets, and compare the resultant trees and alignments to those produced using POY and also maximum likelihood (ML) and maximum parsimony (MP) trees computed on a number of alignments. In general, we find that trees produced by BeeTLe are shorter and more topologically accurate than POY trees, but that neither POY nor BeeTLe produces trees as topologically accurate as ML trees produced on standard alignments. These findings, taken as a whole, suggest that treelength optimization is not as good an approach to phylogenetic tree estimation as maximum likelihood based upon good alignment methods.
format	article
author	Kevin Liu Tandy Warnow
author_facet	Kevin Liu Tandy Warnow
author_sort	Kevin Liu
title	Treelength optimization for phylogeny estimation.
title_short	Treelength optimization for phylogeny estimation.
title_full	Treelength optimization for phylogeny estimation.
title_fullStr	Treelength optimization for phylogeny estimation.
title_full_unstemmed	Treelength optimization for phylogeny estimation.
title_sort	treelength optimization for phylogeny estimation.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/2241f0f1ee33409a80a95f556451fd22
work_keys_str_mv	AT kevinliu treelengthoptimizationforphylogenyestimation AT tandywarnow treelengthoptimizationforphylogenyestimation
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Treelength optimization for phylogeny estimation.

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