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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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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M. Dohrmann, D. Janussen, J. Reitner, A. G. Collins, and G. Worheide Phylogeny and Evolution of Glass Sponges (Porifera, Hexactinellida) Syst Biol, June 1, 2008; 57(3): 388 - 405. [Abstract] [Full Text] [PDF]
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J. J. Wiens, C. A. Kuczynski, S. A. Smith, D. G. Mulcahy, J. W. Sites Jr., T. M. Townsend, and T. W. Reeder Branch Lengths, Support, and Congruence: Testing the Phylogenomic Approach with 20 Nuclear Loci in Snakes Syst Biol, June 1, 2008; 57(3): 420 - 431. [Abstract] [Full Text] [PDF]
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R. Burri, H. N. Hirzel, N. Salamin, A. Roulin, and L. Fumagalli Evolutionary Patterns of MHC Class II B in Owls and Their Implications for the Understanding of Avian MHC Evolution Mol. Biol. Evol., June 1, 2008; 25(6): 1180 - 1191. [Abstract] [Full Text] [PDF]
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N. Wahlberg and C. W. Wheat Genomic Outposts Serve the Phylogenomic Pioneers: Designing Novel Nuclear Markers for Genomic DNA Extractions of Lepidoptera Syst Biol, April 1, 2008; 57(2): 231 - 242. [Abstract] [Full Text] [PDF]
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F. T. Burbrink and R. A. Pyron The Taming of the Skew: Estimating Proper Confidence Intervals for Divergence Dates Syst Biol, April 1, 2008; 57(2): 317 - 328. [Full Text] [PDF]
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I. Ruiz-Trillo, A. J. Roger, G. Burger, M. W. Gray, and B. F. Lang A Phylogenomic Investigation into the Origin of Metazoa Mol. Biol. Evol., April 1, 2008; 25(4): 664 - 672. [Abstract] [Full Text] [PDF]
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A. Zuccaro, C. L. Schoch, J. W. Spatafora, J. Kohlmeyer, S. Draeger, and J. I. Mitchell Detection and Identification of Fungi Intimately Associated with the Brown Seaweed Fucus serratus Appl. Envir. Microbiol., February 15, 2008; 74(4): 931 - 941. [Abstract] [Full Text] [PDF]
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T. A. Isenbarger, M. Finney, C. Rios-Velazquez, J. Handelsman, and G. Ruvkun Miniprimer PCR, a New Lens for Viewing the Microbial World Appl. Envir. Microbiol., February 1, 2008; 74(3): 840 - 849. [Abstract] [Full Text] [PDF]
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T. A. Heath, D. J. Zwickl, J. Kim, and D. M. Hillis Taxon Sampling Affects Inferences of Macroevolutionary Processes from Phylogenetic Trees Syst Biol, February 1, 2008; 57(1): 160 - 166. [Full Text] [PDF]
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