RAxML

Parallel inference of a 10.000-taxon phylogeny with maximum likelihood. Inference of large phylogenetic trees with statistical methods is computationally intensive. We recently introduced simple heuristics which yield accurate trees for synthetic as well as real data and are implemented in a sequential program called RAxML. We have demonstrated that RAxML outperforms the currently fastest statistical phylogeny programs (MrBayes, PHYML) in terms of speed and likelihood values on real data. In this paper we present a non-deterministic parallel implementation of our algorithm which in some cases yields super-linear speedups for an analysis of 1.000 organisms on a LINUX cluster. In addition, we use RAxML to infer a 10.000-taxon phylogenetic tree containing representative organisms from the three domains: Eukarya, Bacteria and Archaea. Finally, we compare the sequential speed and accuracy of RAxML and PHYML on 8 synthetic alignments comprising 4.000 sequences.


References in zbMATH (referenced in 44 articles )

Showing results 21 to 40 of 44.
Sorted by year (citations)
  1. Holland, Barbara R.: The rise of statistical phylogenetics (2013)
  2. Lafond, Manuel; Swenson, Krister M.; El-Mabrouk, Nadia: Error detection and correction of gene trees (2013)
  3. Moret, Bernard M. E.; Lin, Yu; Tang, Jijun: Rearrangements in phylogenetic inference: compare, model, or encode? (2013)
  4. Warnow, Tandy: Large-scale multiple sequence alignment and phylogeny estimation (2013)
  5. Pratas, Frederico; Trancoso, Pedro; Sousa, Leonel; Stamatakis, Alexandros; Shi, Guochun; Kindratenko, Volodymyr: Fine-grain parallelism using multi-core, cell/BE, and GPU systems (2012) ioport
  6. Alachiotis, Nikolaos; Stamatakis, Alexandros: A vector-like reconfigurable floating-point unit for the logarithm (2011) ioport
  7. Brinkmeyer, Malte; Griebel, Thasso; Böcker, Sebastian: Polynomial supertree methods revisited (2011) ioport
  8. Jones, Martin O.; Koutsovoulos, Georgios D.; Blaxter, Mark L.: Iphy: an integrated phylogenetic workbench for supermatrix analyses (2011) ioport
  9. Luecking, Robert K.; Hodkinson, Brendan P.; Stamatakis, Alexandros; Cartwright, Reed A.: PICS-ord: Unlimited coding of ambiguous regions by pairwise identity and cost scores ordination (2011) ioport
  10. Rafique, M. Mustafa; Butt, Ali R.; Nikolopoulos, Dimitrios S.: A capabilities-aware framework for using computational accelerators in data-intensive computing (2011) ioport
  11. JSumner, J. G.; Charleston, M. A.: Phylogenetic estimation with partial likelihood tensors (2010)
  12. Ott, Michael; Stamatakis, Alexandros: Preparing RAxML for the SPEC MPI benchmark suite (2010) ioport
  13. Stöver, Ben C.; Müller, Kai F.: Treegraph 2: combining and visualizing evidence from different phylogenetic analyses (2010) ioport
  14. Wehe, André; Chang, Wen-Chieh; Eulenstein, Oliver; Aluru, Srinivas: A scalable parallelization of the gene duplication problem (2010)
  15. Zierke, Stephanie; Bakos, Jason D.: FPGA acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods (2010) ioport
  16. Williams, Tom A.; Caffrey, Brian E.; Jiang, Xiaowei; Toft, Christina; Fares, Mario A.: Phylogenomic inference of functional divergence (2009) ioport
  17. Langdon, W. B.; Harrison, A. P.: GP on SPMD parallel graphics hardware for mega bioinformatics data mining (2008) ioport
  18. Spray, J.; Hill, J.; Trew, A.: Performance of a lattice quantum chromodynamics kernel on the cell processor (2008) ioport
  19. Stamatakis, A.; Blagojevic, F.; Nikolopoulos, D. S.; Antonopoulos, C. D.: Exploring new search algorithms and hardware for phylogenetics: RAxML meets the IBM cell (2007) ioport
  20. Stamatakis, Alexandros; Auch, Alexander F.; Meier-Kolthoff, Jan; Göker, Markus: Axpcoords & parallel axparafit: Statistical co-phylogenetic analyses on thousands of taxa (2007) ioport

Further publications can be found at: http://www.exelixis-lab.org/