Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees.

Full Abstract

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.

Author information

Author/s: Liu, Kevin (K); Raghavan, Sindhu (S); Nelesen, Serita (S); Linder, C Randal (CR); Warnow, Tandy (T);

Affiliation: Department of Computer Sciences, University of Texas at Austin, One University Station C0500, Austin, TX 78712, USA.

Journal and publication information

Publication Type: Evaluation Studies; Journal Article; Research Support, U.S. Gov't, Non-P.H.S.

Journal: Science (New York, N.Y.) (Science), published in United States. (Language: eng)

Reference: 2009-Jun; vol 324 (issue 5934) : pp 1561-4

Dates: Created 2009/06/22; Completed 2009/06/30;

PMID: 19541996, status: MEDLINE (last retrieval date: 6/30/2009, IMS Date: )

Sourced from the National Library of Medicine. Abstract text and other information may be subject to copyright.

Comments and Corrections

CommentIn: Science. 2009 Jun 19;324(5934):1528-9. (PMID: 19541988)

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Associated Chemicals: DNA (9007-49-2)

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