RAxML swMATH ID: 7716 Software Authors: Stamatakis, Alexandros; Ludwig, Thomas; Meier, Harald Description: 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. Homepage: http://sco.h-its.org/exelixis/web/software/raxml/index.html Source Code: https://github.com/stamatak/standard-RAxML Related Software: MrBayes; BEAST; PAUP*; fastDNAml; R; PHYLIP; ASTRAL-II; FastTree; PAML; PhyML; ClustalW; DendroPy; ape; TNT; CUDA; Rec-I-DCM3; Seq-Gen; Notung; iGTP; INDELible Cited in: 30 Publications Further Publications: http://www.exelixis-lab.org/ all top 5 Cited by 72 Authors 3 Warnow, Tandy J. 2 Kubatko, Laura Salter 2 Matsen, Frederick A. IV 2 Richards, Andrew 2 Stamatakis, Alexandros P. 1 Aizenbud, Yariv 1 Altan-Bonnet, Grégoire 1 Aluru, Srinivas 1 Amsel, Noah 1 Bansal, Mukul Subodh 1 Böcker, Sebastian 1 Bordewich, Magnus 1 Brinkmeyer, Malte 1 Chang, Joseph T. 1 Chang, Wen-Chieh 1 Charleston, Michael A. 1 Christensen, Sarah 1 Collienne, Lena 1 De Maio, Nicola 1 Dinh, Vu 1 El-Mabrouk, Nadia 1 Eulenstein, Oliver 1 Ford, Eric B. 1 Gavryushkin, Alex 1 Gawrychowski, Paweł 1 Griebel, Thasso 1 Guo, Guangbao 1 Hauser, Jörg 1 Holland, Barbara R. 1 Horton, Mitchel D. 1 Jaffe, Ariel 1 JSumner, J. G. 1 Keith, Jonathan M. 1 Kluger, Yuval 1 Kobert, Kassian 1 Kosiol, Carolin 1 Lafond, Manuel 1 Landau, Gad M. 1 Lin, Yu 1 Linz, Simone 1 Lopez, M. Graham 1 Ludwig, Thomas 1 Meier, Harald 1 Minh, Bui Quang 1 Molloy, Erin K. 1 Mora, Thierry 1 Moret, Bernard M. E. 1 Nadler, Boaz 1 Paradis, Emmanuel 1 Pouryahya, Fatemeh 1 Qian, Guoqi 1 Roch, Sébastien 1 Sankoff, David 1 Schrempf, Dominik 1 Semple, Charles 1 Shao, Wei 1 Sly, Allan 1 Spade, David A. 1 St. John, Katherine 1 Sung, Wing-Kin 1 Swenson, Krister M. 1 Tang, Jijun 1 Urheim, Ellen 1 Vachaspati, Pranjal 1 von Haeseler, Arndt 1 Walczak, Aleksandra M. 1 Wehe, André 1 Weimann, Oren 1 Whidden, Chris 1 You, Wenjie 1 Zaman, Sumaira 1 Zhang, Cheng all top 5 Cited in 15 Serials 5 Journal of Theoretical Biology 2 Bulletin of Mathematical Biology 1 Journal of Mathematical Biology 1 Physics Reports 1 Journal of the American Statistical Association 1 Journal of Computational and Applied Mathematics 1 Theoretical Computer Science 1 Probability Theory and Related Fields 1 Algorithmica 1 Journal of Parallel and Distributed Computing 1 Australian & New Zealand Journal of Statistics 1 Statistical Applications in Genetics and Molecular Biology 1 Computational Biology 1 Methods in Molecular Biology 1 SIAM Journal on Mathematics of Data Science all top 5 Cited in 9 Fields 26 Biology and other natural sciences (92-XX) 7 Computer science (68-XX) 5 Statistics (62-XX) 3 Combinatorics (05-XX) 2 General and overarching topics; collections (00-XX) 2 Probability theory and stochastic processes (60-XX) 2 Numerical analysis (65-XX) 1 Linear and multilinear algebra; matrix theory (15-XX) 1 Operations research, mathematical programming (90-XX) Citations by Year