Large-Scale Simultaneous Multiple
Alignment and Phylogeny Estimation.
This project is funded by
NSF DEB 0733029 (ATOL),
and is a
collaboration between the University of
Texas, the University of Georgia, The University of Nebraska,
and the University of Kansas.
Main goals
- New methods for simultaneous estimation of alignments and
trees.
- New simulator tools for evolution which produce
more realistic data (including rearrangements, duplications,
and indels)
- Educational outreach
Project personnel
Senior Personnel:
Students and staff
- Rahul Surhi
- Serita Nelesen
- Kevin Liu
Benchmark datasets
Please go to
-
this page
for various benchmark datasets.
-
this page
for the datasets used to study two-phase methods (Sindhu
Raghavan et al., submitted).
Software
-
The development partitioned version of the GARLI software has been supported
by this award (other software has been written but is not ready for release).
This version is available for testing use by the biological community
from the GARLI wiki hosted by NESCent,
here.
-
SATe (from the Science 2009 paper). Please
see
this page for the SATe software.
The University of Kansas group, headed by
Mark Holder, is creating a new version of
SATe, and it can be accessed
here.
- POY* (see the paper "Barking up the wrong treelength").
This is a
variant of POY that uses a particular affine gap penalty, and
a suitable starting tree, in order to produce more accurate
trees in an efficient way.
(Not yet publically available, but contact us for information on how
to run this.)
- Probtree (see "The effect of the guide tree on multiple
sequence alignments and subsequent phylogenetic analyses"). This
is a variant of ProbCons which uses a particular guide tree
in order to improve the alignment and also the topological accuracy
of the ML tree on the alignment.
(Not yet publically available, but contact us on how to run this.)
Publications
-
K. Liu, S. Nelesen, S. Raghavan, C.R. Linder, and T. Warnow. Barking up the wrong treelength: The impact of gap penalty on alignment and tree accuracy.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, no. 1, pp. 7-21, Jan.-Mar. 2009, doi:10.1109/TCBB.2008.63
-
S. Nelesen, K. Liu, D. Zhao, C. R. Linder, T. Warnow The Effect of the Guide Tree on Multiple Sequence Alignments and Subsequent Phylogenetic Analyses. Pacific Symposium on Biocomputing 13:15-24, 2008. Auxiliary materials available here.
Paper available in
(PDF) form.
-
K. Liu, S. Raghavan, S. Nelesen, C. R. Linder, 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.
See the bottom of this page for a link to the paper.
-
M.T. Holder, J. Sukumaran, P.O. Lewis,
A justification for reporting majority-rule consensus
tree in Bayesian phylogenetics.
Systematic Biology, (2008), 57(5):814-821.
-
H.T. Holder, D.J. Zwickl, C. Dessimoz.
Evaluating the robustness of phylogenetic methods to among-site
variability in substitution processes.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL
SCIENCES, vol. 363, (2008), p. 4013., doi: 10.1098/rstb.2008.016.
News