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 12 articles )

Showing results 1 to 12 of 12.
Sorted by year (citations)

  1. Warnow, Tandy (ed.): Bioinformatics and phylogenetics. Seminal contributions of Bernard Moret (2019)
  2. Whidden, Chris; Iv, Frederick A. Matsen: Efficiently inferring pairwise subtree prune-and-regraft adjacencies between phylogenetic trees (2018)
  3. Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)
  4. Schrempf, Dominik; Minh, Bui Quang; De Maio, Nicola; von Haeseler, Arndt; Kosiol, Carolin: Reversible polymorphism-aware phylogenetic models and their application to tree inference (2016)
  5. Lopez, M. Graham; Horton, Mitchel D.: Batch matrix exponentiation (2014)
  6. 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
  7. Brinkmeyer, Malte; Griebel, Thasso; Böcker, Sebastian: Polynomial supertree methods revisited (2011) ioport
  8. JSumner, J. G.; Charleston, M. A.: Phylogenetic estimation with partial likelihood tensors (2010)
  9. Wehe, André; Chang, Wen-Chieh; Eulenstein, Oliver; Aluru, Srinivas: A scalable parallelization of the gene duplication problem (2010)
  10. Paradis, Emmanuel: Analysis of phylogenetics and evolution with R (2006)
  11. Stamatakis, Alexandros; Ludwig, Thomas; Meier, Harald: RAxML-II: a program for sequential, parallel and distributed inference of large phylogenetic trees (2005) ioport
  12. Stamatakis, Alexandros; Ludwig, Thomas; Meier, Harald: Parallel inference of a 10.000-taxon phylogeny with maximum likelihood (2004)


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