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Dr. Alexandros Stamatakis, Exelixis Lab, Department of Computer Science, Technische Universität München
Tuesday 31 March 2009, 14:30-15:30
Parallel Computation of the Phylogenetic Likelihood Kernel in HW and SW
- 👤 Speaker: Dr. Alexandros Stamatakis, Exelixis Lab, Department of Computer Science, Technische Universität München
- 📅 Date & Time: Tuesday 31 March 2009, 14:30 - 15:30
- 📍 Venue: Mahanakorn Laboratory, EEE
Abstract
The Phylogenetic Likelihood Kernel (PLK) is an important and compute-intensive Bioinformatics function that is used to infer phylogenetic (evolutionary) trees from molecular sequence data. This kernel typically consumes 85-95% of the total run time in algorithms for phylogeny reconstruction which represent a common task in biological data analysis.
I will briefly outline the underlying mathematical ideas at an abstract level. Then, I will describe a dedicated HW architecture to compute the PLK and address parallelization strategies for various computer architectures such as current multi-core systems and the IBM BlueGene/L.
I will conclude with a brief overview of future work and potential topics for joint work.
Series This talk is part of the CAS FPGA Talks series.
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