Accounting for alignment uncertainty in phylogenomics.

Uncertainty in multiple sequence alignments has a large impact on phylogenetic analyses. Little has been done to evaluate the quality of individual positions in protein sequence alignments, which directly impact the accuracy of phylogenetic trees. Here we describe ZORRO, a probabilistic masking prog...

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Autores principales:	Martin Wu, Sourav Chatterji, Jonathan A Eisen
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/a59607bed321484f846adc80ab8fe34a
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id	oai:doaj.org-article:a59607bed321484f846adc80ab8fe34a
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spelling	oai:doaj.org-article:a59607bed321484f846adc80ab8fe34a2021-11-18T07:30:05ZAccounting for alignment uncertainty in phylogenomics.1932-620310.1371/journal.pone.0030288https://doaj.org/article/a59607bed321484f846adc80ab8fe34a2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22272325/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Uncertainty in multiple sequence alignments has a large impact on phylogenetic analyses. Little has been done to evaluate the quality of individual positions in protein sequence alignments, which directly impact the accuracy of phylogenetic trees. Here we describe ZORRO, a probabilistic masking program that accounts for alignment uncertainty by assigning confidence scores to each alignment position. Using the BALIBASE database and in simulation studies, we demonstrate that masking by ZORRO significantly reduces the alignment uncertainty and improves the tree accuracy.Martin WuSourav ChatterjiJonathan A EisenPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 1, p e30288 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Martin Wu Sourav Chatterji Jonathan A Eisen Accounting for alignment uncertainty in phylogenomics.
description	Uncertainty in multiple sequence alignments has a large impact on phylogenetic analyses. Little has been done to evaluate the quality of individual positions in protein sequence alignments, which directly impact the accuracy of phylogenetic trees. Here we describe ZORRO, a probabilistic masking program that accounts for alignment uncertainty by assigning confidence scores to each alignment position. Using the BALIBASE database and in simulation studies, we demonstrate that masking by ZORRO significantly reduces the alignment uncertainty and improves the tree accuracy.
format	article
author	Martin Wu Sourav Chatterji Jonathan A Eisen
author_facet	Martin Wu Sourav Chatterji Jonathan A Eisen
author_sort	Martin Wu
title	Accounting for alignment uncertainty in phylogenomics.
title_short	Accounting for alignment uncertainty in phylogenomics.
title_full	Accounting for alignment uncertainty in phylogenomics.
title_fullStr	Accounting for alignment uncertainty in phylogenomics.
title_full_unstemmed	Accounting for alignment uncertainty in phylogenomics.
title_sort	accounting for alignment uncertainty in phylogenomics.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/a59607bed321484f846adc80ab8fe34a
work_keys_str_mv	AT martinwu accountingforalignmentuncertaintyinphylogenomics AT souravchatterji accountingforalignmentuncertaintyinphylogenomics AT jonathanaeisen accountingforalignmentuncertaintyinphylogenomics
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Accounting for alignment uncertainty in phylogenomics.

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