Parallel Computation of the Phylogenetic Likelihood Kernel in HW and SW

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• Dr. Alexandros Stamatakis, Exelixis Lab, Department of Computer Science, Technische Universität München
• Tuesday 31 March 2009, 14:30-15:30
• Mahanakorn Laboratory, EEE.

If you have a question about this talk, please contact Dr George A Constantinides.

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.

This talk is part of the CAS FPGA Talks series.

This talk is included in these lists:

• CAS FPGA Talks
• Mahanakorn Laboratory, EEE

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