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Multiple Sequence Alignment Methods pp 219–244Cite as

Large-Scale Multiple Sequence Alignment and Tree Estimation Using SATé

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1079))

Abstract

SATé is a method for estimating multiple sequence alignments and trees that has been shown to produce highly accurate results for datasets with large numbers of sequences. Running SATé using its default settings is very simple, but improved accuracy can be obtained by modifying its algorithmic parameters. We provide a detailed introduction to the algorithmic approach used by SATé, and instructions for running a SATé analysis using the GUI under default settings. We also provide a discussion of how to modify these settings to obtain improved results, and how to use SATé in a phylogenetic analysis pipeline.

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Acknowledgments

This work was supported a training fellowship to KL from the Keck Center of the Gulf Coast Consortia, on the NLM Training Program in Biomedical Informatics, National Library of Medicine (NLM) T15LM007093. This work was also partially supported by NSF grant DEB 0733029 to TW.

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Authors and Affiliations

  1. Department of Computer Science, Rice University, Houston, TX, USA

    Kevin Liu

  2. Department of Computer Science, The University of Texas at Austin, Austin, TX, USA

    Tandy Warnow

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  1. Kevin Liu
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  2. Tandy Warnow
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Editors and Affiliations

  1. Dept. of Electrical Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA

    David J Russell

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Liu, K., Warnow, T. (2014). Large-Scale Multiple Sequence Alignment and Tree Estimation Using SATé. In: Russell, D. (eds) Multiple Sequence Alignment Methods. Methods in Molecular Biology, vol 1079. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-646-7_15

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  • DOI: https://doi.org/10.1007/978-1-62703-646-7_15

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  • Publisher Name: Humana Press, Totowa, NJ

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