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BMCBI
2010
142views more  BMCBI 2010»
13 years 5 months ago
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
Background: Likelihood-based phylogenetic inference is generally considered to be the most reliable classification method for unknown sequences. However, traditional likelihood-ba...
Frederick A. Matsen III, Robin B. Kodner, E. Virgi...
PCI
2005
Springer
13 years 11 months ago
Initial Experiences Porting a Bioinformatics Application to a Graphics Processor
Bioinformatics applications are one of the most relevant and compute-demanding applications today. While normally these applications are executed on clusters or dedicated parallel ...
Maria Charalambous, Pedro Trancoso, Alexandros Sta...
IPPS
2006
IEEE
13 years 11 months ago
Phylogenetic models of rate heterogeneity: a high performance computing perspective
Inference of phylogenetic trees using the maximum likelihood (ML) method is NP-hard. Furthermore, the computation of the likelihood function for huge trees of more than 1,000 orga...
Alexandros Stamatakis
SC
1995
ACM
13 years 9 months ago
Parallelizing the Phylogeny Problem
The problem of determining the evolutionary history of species in the form of phylogenetic trees is known as the phylogeny problem. We present a parallelization of the character c...
Jeff A. Jones, Katherine A. Yelick
FPL
2009
Springer
79views Hardware» more  FPL 2009»
13 years 10 months ago
A reconfigurable architecture for the Phylogenetic Likelihood Function
As FPGA devices become larger, more coarse-grain modules coupled with large scale reconfigurable fabric become available, thus enabling new classes of applications to run effici...
Nikolaos Alachiotis, Alexandros Stamatakis, Euripi...