Journal
SCIENCE
Volume 324, Issue 5934, Pages 1561-1564Publisher
AMER ASSOC ADVANCEMENT SCIENCE
DOI: 10.1126/science.1171243
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Funding
- U.S. NSF [DEB 0733029, ITR 0331453, ITR 0121680, EIA 0303609, IGERT 0114387]
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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 SATe (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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