[talks] Colloquium Speaker, Wednesday, February 3, 2010-Tandy Warnow

[Nicole E. Wagenblast]

Speaker: Tandy Warnow, University of Texas at Austin
Title: *Simultaneous Alignment and Phylogenetic Tree Estimation*
Wednesday, February 3, 2010
4:30 PM Small Auditorium (CS 105)

Abstract:
Molecular sequences evolve under processes that include substitutions, 
insertions, and deletions (jointly called \\\"indels\\\"), as well as 
other mechanisms (e.g., duplications and rearrangements). The inference 
of the evolutionary history of these sequences has thus been performed 
in two stages: the first estimates the alignment on the sequences, and 
the second estimates the tree given that alignment. While such methods 
seem to work well on relatively small datasets, these two-stage 
approaches can produce highly incorrect trees and alignments when 
applied to large datasets, or ones that evolve with many indels. In this 
talk, I will present a new method, SATe, that my lab has been developing 
that uses maximum likelihood to estimate the alignment and tree at the 
same time, and that can be used to analyze datasets with up to 1000 
sequences on a desktop in 24 hours. Our study, using both real and 
simulated data, shows that this method produces much more accurate trees 
than the current best methods.

Tandy Warnow is Professor of Computer Sciences at the University of 
Texas at Austin. Her research combines mathematics, computer science, 
and statistics to develop improved models and algorithms for estimating 
complex and large-scale evolutionary histories in both biology and 
historical linguistics. Tandy received her PhD in Mathematics at UC 
Berkeley under the direction of Gene Lawler, and did postdoctoral 
training with Simon Tavare and Michael Waterman at USC. She received the 
National Science Foundation Young Investigator Award in 1994, and the 
David and Lucile Packard Foundation Award in Science and Engineering in 
1996. Tandy is a member of five graduate programs at the University of 
Texas, including Computer Science; Ecology, Evolution, and Behavior; 
Molecular and Cellular Biology; Mathematics; and Computational and 
Applied Mathematics. She is also the director for the multi-disciplinary 
CIPRES (Cyber-Infrastructure for Phylogenetic Research) Project, 
currently funded by the NSF under their Information Technology Program.
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