utcs Phylogenetics
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  • Simultaneous Alignment and Tree Estimation (SATé) is a software package for constructing phylogenies and alignments from sequence data. It is particularly useful for large datasets (hundreds to thousands of sequences), where it has been shown to produce more accurate alignments and trees than previous methods.

    We have just developed PASTA, which is an improvement to SATé - it is faster and more accurate, and can analyze larger datasets (up to 200,000 sequences). We suggest you use PASTA instead of SATé. Contact us if you need assistance.


    The algorithmic designs in SATé and PASTA are under active research development at UTCS by the Warnow Lab (especially with PhD student Siavash Mirarab); the publicly distributed code for SATé is a collaboration with the University of Kansas, under the direction of Mark Holder.

    The public distribution of PASTA is from the Warnow lab, and available at this page.

Software download

  • Please see the Kansas SATé page to download the SATé software, and see the UTCS Phylogenetics website for the PASTA code (which replaces SATé).

  • This page contains datasets and software corresponding to the original SATé submission. (The new version, available through the Kansas website, is both faster and has better accuracy, and we recommend using it instead.)


    K. Liu, S. Raghavan, S. Nelesen, C. R. Linder and T. Warnow. "Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees", Science 324, 1561 (2009) (PDF).

    Liu, K., T.J. Warnow, M.T. Holder, S. Nelesen, J. Yu, A. Stamatakis, and C.R. Linder. "SATe-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees", Systematic Biology, 61(1):90-106, 2011 (PDF).

    Mirarab, S., N. Nguyen, and T. Warnow. "PASTA: ultra-large multiple sequence alignment". Proceedings RECOMB 2014 (PDF).

    Full publication list (some downloadable as PDFs)

Current research

    We are currently developing SATé for amino-acid analyses, for very large datasets (with upwards of 10,000 taxa), and for use with metagenomic data (and next generation sequence data more generally). We welcome research collaborations.

Contact information

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Site help/questions/feedback/requests: e-mail Tandy Warnow