Simultaneous Alignment and Phylogeneic Tree Estimation

SpeakerTandy Warnow (University of Texas-Austin)
SummaryFriday, 3:30 PM at NESCent, Ninth Street and Main Street, Erwin Mill Building, 2024 W. Main Street, Suite A200. For more information, call 919-668-4551. 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.
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