125.RAxML
SPEC MPI2007 Benchmark Description
Benchmark Name
125.RAxML
Benchmark Author
Alexandros Stamatakis [alexandros.stamatakis@epfl.ch]
Benchmark Program General Category
Bioinformatics, Computation of Phylogenetic
(Evolutionary) Trees
Benchmark Description
The program computes large phylogenetic (evolutionary)
trees from alignments of DNA sequence data using the
maximum likelihood method which involves a large
amount of floating point operations. The program has
been parallelized with MPI.
Part of this work has been published
at Supercomputing2002, EuroPar 2004, and at the High Performance Computing
Bioinformatics workshop held in conjunction with IPDPS
(IPDPS2003, IPDPS2004, IPDPS2005). The
program has been used to calculate the largest evolutionary tree to date
containing 10.000 sequences based upon the maximum
likelihood method (see EuroPar 2004 paper).
Input Description
- User starting tree in Newick format.
- A sequence file containing the DNA sequence data for which the phylogenetic tree is
reconstructed.
Output Description
- Reconstructed phylogenetic tree.
Programming Language
C with MPI
Known portability issues
References
- http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm
Last updated: 23 October 2009