Highly Accelerated and Parallelized Version of Parafit for Tests of Host-Parasite Coevolution

[Alexandros Stamatakis <Alexandros.Stamatakis@epfl.ch>]

Dear Users of RAxML,

Please accept my apologies if you consider this message as spam, but
I thought that it might be of interest to some of you:

This is to announce the availability of a highly optimized and parallelized
version of Pierre Legendre's Parafit program, which implements a statistical
test for host-parasite co-evolution (Pierre Legendre, Yves Desdevises,
Eric Bazin: "A Statistical Test for Host-Parasite Coevolution", Systematic Biology
51(2):217-234, 2002.).

The sequential version runs up to 67 times faster than the original Parafit program
while the speedup increases with dataset size. The parallel version scales well up to
128 CPUs on datasets of moderate size. With the parallel version of AxParafit we were able
to conduct the largest Parafit-based analysis to date. The inference took only 8 minutes
as opposed to an estimated runtime of about 4 weeks with Parafit (estimated because the
machine on which Parafit was running crashed).

The software, including a manual, is available as open source code or pre-compiled binaries
at http://icwww.epfl.ch/~stamatak/AxParafit.html .

Best regards,

Alexis
--
Dr. Alexandros Stamatakis

Postdoctoral Researcher
High Performance Computing Bioinformatics

Swiss Federal Institute of Technology
School of Computer & Communication Sciences
Laboratory for Computational Biology and Bioinformatics (LCBB)
STATION 14
CH-1015 Lausanne, Switzerland

Tel:   +41 21 69 31392 (Office)
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Skype: stamatak
Email: Alexandros.Stamatakis@epfl.ch
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