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Literature DB >> 11934758

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing.

Heiko A Schmidt¹, Korbinian Strimmer, Martin Vingron, Arndt von Haeseler.

Abstract

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/).

Entities: Disease

Mesh：

Year: 2002 PMID： 11934758 DOI： 10.1093/bioinformatics/18.3.502

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

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Cited

946 in total

1. Evolution of photosynthetic prokaryotes: a maximum-likelihood mapping approach.

Authors: Jason Raymond; Olga Zhaxybayeva; J Peter Gogarten; Robert E Blankenship
Journal: Philos Trans R Soc Lond B Biol Sci Date: 2003-01-29 Impact factor: 6.237

2. Genetic and electron-microscopic characterization of 'Rickettsiella agriotidis', a new Rickettsiella pathotype associated with wireworm, Agriotes sp. (Coleoptera: Elateridae).

Authors: Andreas Leclerque; Regina G Kleespies; Claudia Ritter; Christina Schuster; Simon Feiertag
Journal: Curr Microbiol Date: 2011-06-03 Impact factor: 2.188

3. Second- and third-hand chloroplasts in dinoflagellates: phylogeny of oxygen-evolving enhancer 1 (PsbO) protein reveals replacement of a nuclear-encoded plastid gene by that of a haptophyte tertiary endosymbiont.

Authors: Ken-ichiro Ishida; Beverley R Green
Journal: Proc Natl Acad Sci U S A Date: 2002-06-27 Impact factor: 11.205

4. Bacterial endosymbiont of the slender pigeon louse, Columbicola columbae, allied to endosymbionts of grain weevils and tsetse flies.

Authors: Takema Fukatsu; Ryuichi Koga; Wendy A Smith; Kohjiiro Tanaka; Naruo Nikoh; Kayoko Sasaki-Fukatsu; Kazunori Yoshizawa; Colin Dale; Dale H Clayton
Journal: Appl Environ Microbiol Date: 2007-08-31 Impact factor: 4.792

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing.

1. Evolution of photosynthetic prokaryotes: a maximum-likelihood mapping approach.

2. Genetic and electron-microscopic characterization of 'Rickettsiella agriotidis', a new Rickettsiella pathotype associated with wireworm, Agriotes sp. (Coleoptera: Elateridae).

3. Second- and third-hand chloroplasts in dinoflagellates: phylogeny of oxygen-evolving enhancer 1 (PsbO) protein reveals replacement of a nuclear-encoded plastid gene by that of a haptophyte tertiary endosymbiont.

4. Bacterial endosymbiont of the slender pigeon louse, Columbicola columbae, allied to endosymbionts of grain weevils and tsetse flies.

5. A phylogenomic investigation of CYCLOIDEA-like TCP genes in the Leguminosae.

6. Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish.

7. Serial recombination during circulation of type 1 wild-vaccine recombinant polioviruses in China.

8. A novel mycovirus that is related to the human pathogen hepatitis E virus and rubi-like viruses.

9. Characterization of hey bHLH genes in teleost fish.

10. Evolution and microsynteny of the apyrase gene family in three legume genomes.