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Science 19 June 2009:
Vol. 324. no. 5934, pp. 1561 - 1564
DOI: 10.1126/science.1171243
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Reports

Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees

Kevin Liu,1 Sindhu Raghavan,1 Serita Nelesen,1 C. Randal Linder,2 Tandy Warnow1,*

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.

1 Department of Computer Sciences, The University of Texas at Austin, One University Station C0500, Austin, TX 78712, USA.
2 Section of Integrative Biology, School of Biological Sciences, The University of Texas at Austin, One University Station C0930, Austin, TX 78712, USA.

* To whom correspondence should be addressed. E-mail: tandy{at}cs.utexas.edu

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THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Uniting Alignments and Trees.
A. Loytynoja and N. Goldman (2009)
Science 324, 1528-1529
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