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

Heiko A. Schmidt(Max Planck Institute for Molecular Genetics), Korbinian Strimmer(University of Oxford), Martin Vingron(Max Planck Institute for Molecular Genetics), Arndt von Haeseler(Max Planck Institute for Evolutionary Anthropology)
Bioinformatics
March 1, 2002
10.1093/bioinformatics/18.3.502
Cited by 2,560Open Access
Full Text

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/).

Related Papers

Evolutionary trees from DNA sequences: A maximum likelihood approach
Joseph Felsenstein|Journal of Molecular Evolution|1981|14.8k
Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.
Koichiro Tamura, M Nei|Molecular Biology and Evolution|1993|11.4k
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
Masami Hasegawa, Hirohisa Kishino, Taka-aki Yano|Journal of Molecular Evolution|1985|8.9k
The rapid generation of mutation data matrices from protein sequences
David T. Jones, William R. Taylor, Janet M. Thornton|Computer applications in the biosciences|1992|7.1k
Amino acid substitution matrices from protein blocks.
Steven Henikoff, Jorja G. Henikoff|Proceedings of the National Academy of Sciences|1992|6.4k