Bioinformatics Vol. 18 no. 3 2002
Pages 502-504
© 2002 Oxford University Press
Applications Note |
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing
1 Max-Planck-Institut
für Molekulare Genetik, Ihnestr. 73,
D-14195 Berlin, Germany
2 University of Oxford, Department of
Zoology, South Parks Road, Oxford OX1 3PS, UK
3 Max-Planck-Institut
für
Evolutionäre Anthropologie, Inselstr.
22, D-04103 Leipzig, Germany
Received on August 5, 2001
; revised on September 20, 2001
; accepted on October 9, 2001
Summary: TREE-PUZZLE is a program package for quartet-based maximum-likelihood phylogenetic analysis (formerly PUZZLE, Strimmer and von Haeseler, Mol. Biol. Evol. , 13, 964–969, 1996) that provides methods for reconstruction, comparison, and testing of trees and models on DNA as well as protein sequences. To reduce waiting time for larger datasets the tree reconstruction part of the software has been parallelized using message passing that runs on clusters of workstations as well as parallel computers.
Availability: http://www.tree-puzzle.de. The program is written in ANSI C. TREE-PUZZLE can be run on UNIX, Windows and Mac systems, including Mac OS X. To run the parallel version of PUZZLE, a Message Passing Interface (MPI) library has to be installed on the system. Free MPI implementations are available on the Web (cf. http://www.lam-mpi.org/mpi/implementations/).
Contact: hschmidt{at}molgen.mpg.de; haeseler{at}eva.mpg.de
* To whom correspondence should be addressed.
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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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M. T. Edwards, N. K. Fry, and T. G. Harrison Clonal population structure of Legionella pneumophila inferred from allelic profiling Microbiology, March 1, 2008; 154(3): 852 - 864. [Abstract] [Full Text] [PDF]
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H. Zhang, D. Bhattacharya, L. Maranda, and S. Lin Mitochondrial cob and cox1 Genes and Editing of the Corresponding mRNAs in Dinophysis acuminata from Narragansett Bay, with Special Reference to the Phylogenetic Position of the Genus Dinophysis Appl. Envir. Microbiol., March 1, 2008; 74(5): 1546 - 1554. [Abstract] [Full Text] [PDF]
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S. Arai, S. N. Bennett, L. Sumibcay, J. A. Cook, J.-W. Song, A. Hope, C. Parmenter, V. R. Nerurkar, T. L. Yates, and R. Yanagihara Phylogenetically Distinct Hantaviruses in the Masked Shrew (Sorex cinereus) and Dusky Shrew (Sorex monticolus) in the United States Am J Trop Med Hyg, February 1, 2008; 78(2): 348 - 351. [Abstract] [Full Text] [PDF]
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G. P. Fournier and J. P. Gogarten Evolution of Acetoclastic Methanogenesis in Methanosarcina via Horizontal Gene Transfer from Cellulolytic Clostridia J. Bacteriol., February 1, 2008; 190(3): 1124 - 1127. [Abstract] [Full Text] [PDF]
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G. S. Vernikos and J. Parkhill Resolving the structural features of genomic islands: A machine learning approach Genome Res., February 1, 2008; 18(2): 331 - 342. [Abstract] [Full Text] [PDF]
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N. Nikoh, K. Tanaka, F. Shibata, N. Kondo, M. Hizume, M. Shimada, and T. Fukatsu Wolbachia genome integrated in an insect chromosome: Evolution and fate of laterally transferred endosymbiont genes Genome Res., February 1, 2008; 18(2): 272 - 280. [Abstract] [Full Text] [PDF]
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J. W. Leigh, E. Susko, M. Baumgartner, and A. J. Roger Testing Congruence in Phylogenomic Analysis Syst Biol, February 1, 2008; 57(1): 104 - 115. [Abstract] [Full Text] [PDF]
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D. Kerk, G. Templeton, and G. B.G. Moorhead Evolutionary Radiation Pattern of Novel Protein Phosphatases Revealed by Analysis of Protein Data from the Completely Sequenced Genomes of Humans, Green Algae, and Higher Plants Plant Physiology, February 1, 2008; 146(2): 351 - 367. [Abstract] [Full Text] [PDF]
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 L. B. Kent, K. K.O. Walden, and H. M. Robertson The Gr Family of Candidate Gustatory and Olfactory Receptors in the Yellow-Fever Mosquito Aedes aegypti Chem Senses, January 1, 2008; 33(1): 79 - 93. [Abstract] [Full Text] [PDF]
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D. R. Scannell and K. H. Wolfe A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast Genome Res., January 1, 2008; 18(1): 137 - 147. [Abstract] [Full Text] [PDF]
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N. Molina and E. van Nimwegen Universal patterns of purifying selection at noncoding positions in bacteria Genome Res., January 1, 2008; 18(1): 148 - 160. [Abstract] [Full Text] [PDF]
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H. Takahashi, A. Kamiya, A. Ishiguro, A. C. Suzuki, N. Saitou, A. Toyoda, and J. Aruga Conservation and Diversification of Msx Protein in Metazoan Evolution Mol. Biol. Evol., January 1, 2008; 25(1): 69 - 82. [Abstract] [Full Text] [PDF]
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C. Ameline-Torregrosa, B.-B. Wang, M. S. O'Bleness, S. Deshpande, H. Zhu, B. Roe, N. D. Young, and S. B. Cannon Identification and Characterization of Nucleotide-Binding Site-Leucine-Rich Repeat Genes in the Model Plant Medicago truncatula Plant Physiology, January 1, 2008; 146(1): 5 - 21. [Abstract] [Full Text] [PDF]
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R. F. Mills, M. L. Doherty, R. L. Lopez-Marques, T. Weimar, P. Dupree, M. G. Palmgren, J. K. Pittman, and L. E. Williams ECA3, a Golgi-Localized P2A-Type ATPase, Plays a Crucial Role in Manganese Nutrition in Arabidopsis Plant Physiology, January 1, 2008; 146(1): 116 - 128. [Abstract] [Full Text] [PDF]
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Z. Lin, M. Nei, and H. Ma The origins and early evolution of DNA mismatch repair genes multiple horizontal gene transfers and co-evolution Nucleic Acids Res., December 3, 2007; 35(22): 7591 - 7603. [Abstract] [Full Text] [PDF]
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D. A. Morrison Increasing the Efficiency of Searches for the Maximum Likelihood Tree in a Phylogenetic Analysis of up to 150 Nucleotide Sequences Syst Biol, December 1, 2007; 56(6): 988 - 1010. [Abstract] [Full Text] [PDF]
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M. D. Rasmussen and M. Kellis Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes Genome Res., December 1, 2007; 17(12): 1932 - 1942. [Abstract] [Full Text] [PDF]
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