Materials for the Science paper

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, vol. 324, no. 5934, pp. 1561-1564, 19 June 2009, doi: 10.1126/science.1171243. 2009.

To reach the SATe software download page, please click here.

We have improved SATe since it was developed. The most recent version is called PASTA (Practical Alignments using SATe and TRansitivity). PASTA is faster, can analyze larger datasets (up to 200,000 sequences), and is more accurate. PASTA is available as open-source software, and uses a very similar GUI as SATe. We recommend you use PASTA instead of SATe. The paper for PASTA is available here.

This study was partially supported by

NSF DEB 0733029 (ATOL): Large-Scale Simultaneous Multiple Alignment and Phylogeny Estimation. See the project webpage for more information.
NSF ITR 0331453 (Large): Building the Tree of Life -- A National Resource for Phyloinformatics and Computational Phylogenetics (see CIPRES.

For datasets (real and biological) and software used in the paper, please see this page.