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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

Heiko A. Schmidt 1, Korbinian Strimmer 2, Martin Vingron 1 and Arndt von Haeseler 3,*

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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J. Gen. Virol.Home page
S. Noppornpanth, Y. Poovorawan, T. X. Lien, S. L. Smits, A. D. M. E. Osterhaus, and B. L. Haagmans
Complete genome analysis of hepatitis C virus subtypes 6t and 6u
J. Gen. Virol., May 1, 2008; 89(5): 1276 - 1281.
[Abstract] [Full Text] [PDF]


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J. Bacteriol.Home page
M. Pilhofer, K. Rappl, C. Eckl, A. P. Bauer, W. Ludwig, K.-H. Schleifer, and G. Petroni
Characterization and Evolution of Cell Division and Cell Wall Synthesis Genes in the Bacterial Phyla Verrucomicrobia, Lentisphaerae, Chlamydiae, and Planctomycetes and Phylogenetic Comparison with rRNA Genes
J. Bacteriol., May 1, 2008; 190(9): 3192 - 3202.
[Abstract] [Full Text] [PDF]


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Proc. Natl. Acad. Sci. USAHome page
L. D. Alcaraz, G. Olmedo, G. Bonilla, R. Cerritos, G. Hernandez, A. Cruz, E. Ramirez, C. Putonti, B. Jimenez, E. Martinez, et al.
The genome of Bacillus coahuilensis reveals adaptations essential for survival in the relic of an ancient marine environment
PNAS, April 15, 2008; 105(15): 5803 - 5808.
[Abstract] [Full Text] [PDF]


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Int. J. Syst. Evol. Microbiol.Home page
A. Leclerque and R. G. Kleespies
16S rRNA-, GroEL- and MucZ-based assessment of the taxonomic position of 'Rickettsiella melolonthae' and its implications for the organization of the genus Rickettsiella
Int J Syst Evol Microbiol, April 1, 2008; 58(4): 749 - 755.
[Abstract] [Full Text] [PDF]


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Appl. Environ. Microbiol.Home page
C. Knief, L. Frances, F. Cantet, and J. A. Vorholt
Cultivation-Independent Characterization of Methylobacterium Populations in the Plant Phyllosphere by Automated Ribosomal Intergenic Spacer Analysis
Appl. Envir. Microbiol., April 1, 2008; 74(7): 2218 - 2228.
[Abstract] [Full Text] [PDF]


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Mol Biol EvolHome page
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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CSH ProtocolsHome page
D. W. Mount
The Maximum Likelihood Approach for Phylogenetic Prediction
CSH Protocols, April 1, 2008; 2008(5): pdb.top34 - pdb.top34.
[Abstract] [Full Text]


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MicrobiologyHome page
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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Appl. Environ. Microbiol.Home page
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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J R Soc InterfaceHome page
P. R Kensche, V. van Noort, B. E Dutilh, and M. A Huynen
Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution
J R Soc Interface, February 6, 2008; 5(19): 151 - 170.
[Abstract] [Full Text] [PDF]


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Am J Trop Med HygHome page
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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J. Bacteriol.Home page
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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Genome ResHome page
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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Genome ResHome page
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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Syst BiolHome page
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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Plant Physiol.Home page
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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Chem SensesHome page
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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Genome ResHome page
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.
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Genome ResHome page
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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Mol Biol EvolHome page
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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Plant Physiol.Home page
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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Plant Physiol.Home page
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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Physiol. GenomicsHome page
D. Ikeda, Y. Ono, P. Snell, Y. J. K. Edwards, G. Elgar, and S. Watabe
Divergent evolution of the myosin heavy chain gene family in fish and tetrapods: evidence from comparative genomic analysis
Physiol Genomics, December 19, 2007; 32(1): 1 - 15.
[Abstract] [Full Text] [PDF]


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Nucleic Acids ResHome page
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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Syst BiolHome page
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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DevelopmentHome page
H. Bielen, S. Oberleitner, S. Marcellini, L. Gee, P. Lemaire, H. R. Bode, R. Rupp, and U. Technau
Divergent functions of two ancient Hydra Brachyury paralogues suggest specific roles for their C-terminal domains in tissue fate induction
Development, December 1, 2007; 134(23): 4187 - 4197.
[Abstract] [Full Text] [PDF]


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Genome ResHome page
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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