SATé and PASTA
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
The public distribution of PASTA is from the Warnow lab,
and available at this page.
Please see the
Kansas SATé page to download the SATé software,
and see the UTCS Phylogenetics website for the PASTA code (which replaces SATé).
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)
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
Mirarab, S., N. Nguyen, and T. Warnow. "PASTA: ultra-large
multiple sequence alignment". Proceedings RECOMB 2014
Full publication list
(some downloadable as PDFs)
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
We welcome research collaborations.
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