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Abstract Detail


BSA Past-Presidentís Symposium: Computational Issues and Solutions for the Study of Plant Phylogeny

Warnow, Tandy [1], Linder, Randal [2].

A new method for simultaneous estimation of alignments and phylogenies on large, difficult-to-align datasets.

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 usually been performed in two stages: first an alignment is estimated on the sequences, and then a tree is estimated given that alignment. While such methods often work well on relatively small datasets, they can produce highly incorrect trees and alignments when applied to large datasets or ones which evolve rapidly and/or with many indels. In this talk, we will present a new method that we have 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 computer in 24 hours. Our studies, using both real and simulated data, show that this method produces much more accurate trees and alignments than the current best methods on highly diverged, gappy sequences.


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Related Links:
CIPRES project webpage
Warnow home page


1 - University of Texas at Austin, Computer Science, Austin, Texas, 78712, USA
2 - University of Texas Austin, Section of Integrative Biology, 1 University Station, A6700, Austin, Texas, 78712-7640, USA

Keywords:
large data sets
alignment.

Presentation Type: Symposium or Colloquium Presentation
Session: SY9
Location: Ballroom 2/Cliff Lodge - Level B
Date: Wednesday, July 29th, 2009
Time: 9:00 AM
Number: SY9002
Abstract ID:1036


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