SATé
Overview
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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 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
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Please see the
Kansas SATé page to download the software.
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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).
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.
May 20 and 21, 2012,
Smithsonian Institution, Washington, DC
The workshop is funded by the National Science Foundation
through grant
DEB 0733029
to the University of Texas.
Registration is required, and attendance is limited to 40 participants.
The workshop will include presentations of new methods for
multiple sequence alignment and phylogeny estimation,
also training in the use of these methods, and personal
assistance in analyzing datasets using the SATé software.
Applications for the workshop (and for travel support) are
due by February 15, 2012, and will be responded to by
March 1. We expect to be able to provide support to all
attendees.
Please click here
for the application form.
Contact information
Please contact Tandy Warnow
by email at "tandy" at "cs.utexas.edu".
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