Overview

• 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 other methods.

Developers

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

Software download

• Please see the Kansas SATé page to download the software.


• 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.)

Publications

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).

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

Please contact Tandy Warnow by email at "tandy" at "cs.utexas.edu".