Title: Rapid Parallel Evolutionary Placement of Short Sequence Reads Speaker: Dr. Alexandros "Alexis" Stamatakis, Technische Universität München Date/Time: Tuesday, March 30, 2010, 10:00 am Location: CSRI Building/Room 90 (Sandia NM) Brief Abstract: The current multi-core revolution in computer architectures in combination with the biological data tsunami that is driven by new wet-lab techniques such as the 454 or Solexa sequencers pose new challenges for the field of large-scale phylogenetic inference. To this end, I will outline a new sequential and parallel algorithm that can be used to accurately place short reads as obtained for instance from microbial samples into a phylogenetic reference tree by Maximum Likelihood. Apart from the parallelization of this specific algorithm I will also cover general problems and solutions regarding the parallelization of the phylogenetic Maximum Likelihood function including load balance issues and hybrid Pthreads/MPI implementations of the RAxML and MrBayes phylogenetics codes.CSRI POC: Danny Rintoul, (505) 844-9592 & Nicholas Pattengale (505) 284-9352 |