Bioinformatics Advance Access published online on August 23, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl446
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1 Swiss Federal Institute of Technology Lausanne, School of Computer & Communication Sciences, Lab Prof. Moret, STATION 14, CH-1015 Lausanne, Switzerland
* To whom correspondence should be addressed.
Summary: RAxML-VI-HPC (Randomized Axelerated Maximum Likelihood for High Performance Computing) is a sequential and parallel program for inference of large phylogenies with Maximum Likelihood (ML). Low-level technical optimizations, a modification of the search algorithm, and the use of the GTR+CAT approximation as replacement for GTR+ Availability: diwww.epfl.ch/~stamatak.
Received May 15, 2006
Revised July 21, 2006
Accepted August 16, 2006
Applications note
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Alexandros Stamatakis 1 *
Alexandros Stamatakis, E-mail: Alexandros.Stamatakis{at}epfl.ch
Abstract 
yield a program that is between 2.7 and 52 times faster than the previous version of RAxML. A large-scale performance comparison with GARLI, PHYML, IQPNNI, and MrBayes on real data containing 1,000 up to 6,722 taxa shows that RAxML requires at least 5.6 times less main memory and yields better trees in similar times than the best competing program (GARLI) on datasets up to 2,500 taxa. On datasets 
4,000 taxa it also runs 2-3 times faster than GARLI. RAxML has been parallelized with MPI to conduct parallel multiple bootstraps and inferences on distinct starting trees. The program has been used to compute ML trees on two of the largest alignments to date containing 25,057 (1,463 bp) and 2,182 (51,089 bp) taxa respectively.
Associate Editor: Keith A Crandall
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N. Poulakakis, S. Glaberman, M. Russello, L. B. Beheregaray, C. Ciofi, J. R. Powell, and A. Caccone From the Cover: Historical DNA analysis reveals living descendants of an extinct species of Galapagos tortoise PNAS, October 7, 2008; 105(40): 15464 - 15469. [Abstract] [Full Text] [PDF]
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S. A. Smith and M. J. Donoghue Rates of Molecular Evolution Are Linked to Life History in Flowering Plants Science, October 3, 2008; 322(5898): 86 - 89. [Abstract] [Full Text] [PDF]
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J. Kim and M. J. Sanderson Penalized Likelihood Phylogenetic Inference: Bridging the Parsimony-Likelihood Gap Syst Biol, October 1, 2008; 57(5): 665 - 674. [Abstract] [Full Text] [PDF]
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A. Stamatakis, P. Hoover, and J. Rougemont A Rapid Bootstrap Algorithm for the RAxML Web Servers Syst Biol, October 1, 2008; 57(5): 758 - 771. [Abstract] [Full Text] [PDF]
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S. S. Renner, G. W. Grimm, G. M. Schneeweiss, T. F. Stuessy, and R. E. Ricklefs Rooting and Dating Maples (Acer) with an Uncorrelated-Rates Molecular Clock: Implications for North American/Asian Disjunctions Syst Biol, October 1, 2008; 57(5): 795 - 808. [Abstract] [Full Text] [PDF]
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E. Roberts, A. Sethi, J. Montoya, C. R. Woese, and Z. Luthey-Schulten Molecular signatures of ribosomal evolution PNAS, September 16, 2008; 105(37): 13953 - 13958. [Abstract] [Full Text] [PDF]
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J. Harshman, E. L. Braun, M. J. Braun, C. J. Huddleston, R. C. K. Bowie, J. L. Chojnowski, S. J. Hackett, K.-L. Han, R. T. Kimball, B. D. Marks, et al. Phylogenomic evidence for multiple losses of flight in ratite birds PNAS, September 9, 2008; 105(36): 13462 - 13467. [Abstract] [Full Text] [PDF]
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A. B. Prasad, M. W. Allard, NISC Comparative Sequencing Program, and E. D. Green Confirming the Phylogeny of Mammals by Use of Large Comparative Sequence Data Sets Mol. Biol. Evol., September 1, 2008; 25(9): 1795 - 1808. [Abstract] [Full Text] [PDF]
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S. D'Aniello, M. Irimia, I. Maeso, J. Pascual-Anaya, S. Jimenez-Delgado, S. Bertrand, and J. Garcia-Fernandez Gene Expansion and Retention Leads to a Diverse Tyrosine Kinase Superfamily in Amphioxus Mol. Biol. Evol., September 1, 2008; 25(9): 1841 - 1854. [Abstract] [Full Text] [PDF]
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F. Burki, K. Shalchian-Tabrizi, and J. Pawlowski Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes Biol Lett, August 23, 2008; 4(4): 366 - 369. [Abstract] [Full Text] [PDF]
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L. Gomez-Alpizar, C.-H. Hu, R. Oliva, G. Forbes, and J. B. Ristaino Phylogenetic relationships of Phytophthora andina, a new species from the highlands of Ecuador that is closely related to the Irish potato famine pathogen Phytophthora infestans Mycologia, July 1, 2008; 100(4): 590 - 602. [Abstract] [Full Text] [PDF]
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S. J. Hackett, R. T. Kimball, S. Reddy, R. C. K. Bowie, E. L. Braun, M. J. Braun, J. L. Chojnowski, W. A. Cox, K.-L. Han, J. Harshman, et al. A Phylogenomic Study of Birds Reveals Their Evolutionary History Science, June 27, 2008; 320(5884): 1763 - 1768. [Abstract] [Full Text] [PDF]
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