B&MSSS: New Phylogenetic Placement and Taxon Identification Methods for Metagenomic Data - Jul. 2012

SAND Number: SAND2012-3307P Internal Release Only Presenter: Dr. Tandy Warnow Bioscience/Material Science Speaker Series (B&MSSS) Phylogenetic placement arises in the analysis of metagenomic data, in which the objective is to insert short molecular sequences (called "query sequences") into an existing phylogenetic tree and alignment on full-length sequences for the same gene. We present SEPP, a general ``boosting" technique to improve the accuracy and/or speed of phylogenetic placement techniques. The key algorithmic aspect of SEPP is a dataset decomposition technique in SATe (Liu et al., Science 2009 and Systematic Biology (in press), a method that utilizes an iterative divide-and-conquer technique to co-estimate alignments and trees on large molecular sequence datasets. We show that SEPP improves current phylogenetic placement methods, placing metagenomic sequences more accurately when the set of input sequences has a large evolutionary diameter and produces placements of comparable accuracy in a fraction of the time for easier cases. We then show that a combination of Metaphyler (Liu et al, BMC Genomics 2011) and SEPP produces dramatically improved accuracy over all current taxon identification methods. Joint work with Siavash Mirarab and Nam Nguyen, PhD students at UT-Austin, and Bo Liu and Mihai Pop at the University of Maryland.

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7/18/2012 2:25:00 PM