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

• Published in: Bioinformatics 2002-03, Vol.18 (3), p.502-504
• Main Authors: Schmidt, Heiko A., Strimmer, Korbinian, Vingron, Martin, von Haeseler, Arndt
• Format: Article
• Language: English
• Subjects: Algorithms; Biological and medical sciences; Computing Methodologies; Database Management Systems; Databases, Genetic; Fundamental and applied biological sciences. Psychology; General aspects; Internet; Likelihood Functions; Mathematical Computing; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Molecular Sequence Data; Phylogeny; Sequence Analysis - methods; Sequence Analysis - statistics & numerical data; Software
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/18.3.502

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: [e-mail]; [e-mail] * To whom correspondence should be addressed.