Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies
نویسندگان
چکیده
A versatile method, quartet puzzling, is introduced to reconstruct the topology (branching pattern) of a phylogenetic tree based on DNA or amino acid sequence data. This method applies maximum-likelihood tree reconstruction to all possible quartets that can be formed from n sequences. The quartet trees serve as starting points to reconstruct a set of optimal n-taxon trees. The majority rule consensus of these trees defines the quartet puzzling tree and shows groupings that are well supported. Computer simulations show that the performance of quartet puzzling to reconstruct the true tree is always equal to or better than that of neighbor joining. For some cases with high transition/transversion bias quartet puzzling outperforms neighbor joining by a factor of 10. The application of quartet puzzling to mitochondrial RNA and tRNAVd’ sequences from amniotes demonstrates the power of the approach. A PHYLIP-compatible ANSI C program, PUZZLE, for analyzing nucleotide or amino acid sequence data is available.
منابع مشابه
Letter to the Editor Bayesian Probabilities and Quartet Puzzling
Quartet puzzling (QP), a heuristic tree search procedure for maximum-likelihood trees, has recently been introduced (Strimmer and von Haeseler 1996). This method uses maximum-likelihood criteria for quartets of taxa which are then combined to form trees based on larger numbers of taxa. Thus, QP can be practically applied to data sets comprising a much greater number of taxa than can other searc...
متن کاملRandom Tree-Puzzle leads to the Yule-Harding distribution.
Approaches to reconstruct phylogenies abound and are widely used in the study of molecular evolution. Partially through extensive simulations, we are beginning to understand the potential pitfalls as well as the advantages of different methods. However, little work has been done on possible biases introduced by the methods if the input data are random and do not carry any phylogenetic signal. A...
متن کاملShort Quartet Puzzling: A New Quartet-Based Phylogeny Reconstruction Algorithm
Quartet-based phylogeny reconstruction methods, such as Quartet Puzzling, were introduced in the hope that they might be competitive with maximum likelihood methods, without being as computationally intensive. However, despite the numerous quartet-based methods that have been developed, their performance in simulation has been disappointing. In particular, Ranwez and Gascuel, the developers of ...
متن کاملMaximum-likelihood analysis using TREE-PUZZLE.
TREE-PUZZLE provides a means to analyze and reconstruct evolutionary relationships and trees based on quartets, i.e., groups of four sequences. Basic Protocol 1 explains how to reconstruct trees based on the maximum-likelihood principle and quartet puzzling. Basic Protocol 2 discusses likelihood mapping, a method to visualize phylogenetic content in a multiple sequence alignment. Basic Protocol...
متن کاملA Global Maximum Likelihood Super-Quartet Phylogeny Method
Extending the idea of our previous algorithm [17, 18] we developed a new sequential quartet-based phylogenetic tree construction method. This new algorithm reconstructs the phylogenetic tree iteratively by examining at each merge step every possible super-quartet which is formed by four subtrees instead of simple quartet in our previous algorithm. Because our new algorithm evaluates super-quart...
متن کامل