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

Heiko A Schmidt; Korbinian Strimmer; Martin Vingron; Arndt von Haeseler

doi:10.1093/bioinformatics/18.3.502

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

Bioinformatics. 2002 Mar;18(3):502-4. doi: 10.1093/bioinformatics/18.3.502.

Authors

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

Affiliation

¹ Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, D-14195 Berlin, Germany. hschmidt@eva.mpg.de

PMID: 11934758
DOI: 10.1093/bioinformatics/18.3.502

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/).

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Computing Methodologies
Database Management Systems*
Databases, Genetic
Internet
Likelihood Functions*
Mathematical Computing*
Molecular Sequence Data
Phylogeny
Sequence Analysis / methods*
Sequence Analysis / statistics & numerical data
Software*