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

Heiko A. SchmidtMax-Planck-Institut für Molekulare Genetik, Ihnestr. 73, D-14195 Berlin, Germany. [email protected]Korbinian StrimmerUniversity of Oxford, Department of Zoology, South Parks Road, Oxford OX1 3PS, UK andMartin VingronMax-Planck-Institut f r Molekulare Genetik, Ihnestr. 73, D-14195 Berlin, Germany,Arndt von HaeselerMax-Planck-Institut f r Evolution re Anthropologie, Inselstr. 22, D-04103 Leipzig, Germany

2002en

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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/).

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DOI: 10.1093/bioinformatics/18.3.502

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