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DateTuesday, August 18, 2009
Time2:00 pm
LocationGS 906
DetailsThe committee members are:
Co-Advisors: John Kececioglu, Mike Sanderson
Alon Efrat
Bongki Moon
David Maddison
SpeakerTravis Wheeler
TitlePhD Dissertation Thesis Defense
AffiliationComputer Science Department

Efficient Construction of Accurate Multiple Alignments and Large-Scale Neighbor-Joining Phylogenies

A central focus of computational biology is to organize and make use
of vast stores of molecular sequence data. Two of the most
well-studied and fundamental problems in the field are sequence
alignment and phylogeny inference. The problem of sequence alignment
is to take a set of DNA, RNA, or protein sequences and identify
related segments of these sequences. Perhaps the most common use of
alignments of multiple sequences is as input for methods designed to
infer a phylogeny, or tree describing the evolutionary history of the

Efficient computation of high-quality alignments, and of high-quality
phylogenies based on those alignments, are both open problems in the
field of computational biology. The two topics are circularly related:
standard phylogeny inference methods take a multiple sequence
alignment as input, while computation of a rudimentary phylogeny is a
step in the standard sequence alignment method. My dissertation deals
with these topics, exploring a wide range of methods applied to
aligning multiple sequences, as well as an approach that dramatically
increases the speed and scalability of a common method for phylogeny