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[Colloquium] Parallel Computing in Phylogenetic Tree Reconstruction

April 1, 2010

Watch Colloquium: 

Quicktime file (523 MB)
AVI file (514 MB)


  • Date: Thursday, April 1st, 2010 
  • Time: 11 am — 12:15 pm 
  • Place: Mechanical Engineering, Room 218

Alexandros Stamatakis
Department of Computer Science Technical University of Munich

Abstract:

Abstract: The reconstruction of phylogenetic (evolutionary) trees from molecular sequence data under the Maximum Likelihood model represents a compute and memory intensive task.

In this talk I will address how to orchestrate the phylogenetic likelihood function on a large variety of parallel architectures ranging from FPGAs, over multi-core processors, to the IBM BlueGene architecture. I will also address the challenges of maintaining a production level sequential and parallel open-source code for phylogeny reconstruction and discuss some interesting bugs. I will conclude with future challenges in the field.