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.
KeywordsParallel Implementation Parallel Inference Good Likelihood Bayesian Phylogenetic Inference Rearrangement Step
Unable to display preview. Download preview PDF.
- 7.Olsen, G., et al.: fastdnaml: A Tool for Construction of Phylogenetic Trees of DNA Sequences using Maximum Likelihood. Comput. Appl. Biosci. 10, 41–48 (1994)Google Scholar
- 8.PAUP: paup.csit.fsu.edu (visited May 2003)Google Scholar
- 9.PHYLIP: evolution.genetics.washington.edu (visited November 2003) Google Scholar
- 10.RRZE, www.rrze.uni-erlangen.de (visited October 2003)
- 11.Stamatakis, A., et al.: New Fast and Accurate Heuristics for Inference of Large Phylogenetic Trees. In: Proc. of IPDPS (2004)Google Scholar
- 12.Stamatakis, A., et al.: RAxML-III: A Fast Program for Maximum Likelihood-based Inference of Large Phylogenetic Trees. Bioinf. (to be published)Google Scholar
- 13.Stewart, C., et al.: Parallel Implementation and Performance of fastdnaml - a Program for Maximum Likelihood Phylogenetic Inference. In: Proc. of SC 2001 (2001)Google Scholar
- 14.Strimmer, K., et al.: Quartet Puzzling: A Maximum-Likelihood Method for Reconstructing Tree Toologies. Mol. Biol. Evol. 13, 964–969 (1996)Google Scholar
- 15.Williams, T.L., et al.: An Investigation of Phylogenetic Likelihood Methods. In: Proc. of BIBE 2003 (2003)Google Scholar