| Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. | |
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MedLine Citation:
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PMID: 19541996 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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Inferring an accurate evolutionary tree of life requires high-quality alignments of molecular sequence data sets from large numbers of species. However, this task is often difficult, slow, and idiosyncratic, especially when the sequences are highly diverged or include high rates of insertions and deletions (collectively known as indels). We present SATé (simultaneous alignment and tree estimation), an automated method to quickly and accurately estimate both DNA alignments and trees with the maximum likelihood criterion. In our study, it improved tree and alignment accuracy compared to the best two-phase methods currently available for data sets of up to 1000 sequences, showing that coestimation can be both rapid and accurate in phylogenetic studies. |
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Authors:
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Kevin Liu; Sindhu Raghavan; Serita Nelesen; C Randal Linder; Tandy Warnow |
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Publication Detail:
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Type: Evaluation Studies; Journal Article; Research Support, U.S. Gov't, Non-P.H.S. |
Journal Detail:
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Title: Science (New York, N.Y.) Volume: 324 ISSN: 1095-9203 ISO Abbreviation: Science Publication Date: 2009 Jun |
Date Detail:
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Created Date: 2009-06-22 Completed Date: 2009-06-30 Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 0404511 Medline TA: Science Country: United States |
Other Details:
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Languages: eng Pagination: 1561-4 Citation Subset: IM |
Affiliation:
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Department of Computer Sciences, University of Texas at Austin, One University Station C0500, Austin, TX 78712, USA. |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Algorithms Automation Computer Simulation DNA Evolution, Molecular Likelihood Functions Phylogeny* Sequence Alignment* / methods Software* |
| Chemical | |
Reg. No./Substance:
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9007-49-2/DNA |
| Comments/Corrections | |
Comment In:
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Science. 2009 Jun 19;324(5934):1528-9
[PMID:
19541988
]
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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