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

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