CS Colloquium
Thursday, January 28, 2010
10:30 a.m., AKW 200

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Speaker: Tandy Warnow, Department of Computer Sciences
The University of Texas at Austin

Title: Simultaneous Alignment and Phylogenetic Tree Estimation

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.

Joint work with Kevin Liu, Sindhu Raghavan, Serita Nelesen, and Randy Linder.

Bio: 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 reconstructing complex and large-scale evolutionary histories in both biology and historical linguistics. She has served on several national and international boards, including the International Society for Computational Biology, and was the Co-Director of the Center for Computational Biology and Bioinformatics at the University of Texas at Austin.

Tandy received the National Science Foundation Young Investigator Award in 1994, and the David and Lucile Packard Foundation Award in Science and Engineering in 1996. She is currently focusing her efforts on the CIPRES Project (http://www.phylo.org, Cyber-Infrastructure for Phylogenetic Research), which is an NSF-funded project to help build a national computational infrastructure for large-scale phylogenetic reconstruction.