TREE-PUZZLE (previously known as PUZZLE) is an interactive console program that implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch.
TREE-PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can also be calculated under the clock-assumption. In addition, TREE-PUZZLE offers a novel method, likelihood mapping, to investigate the support of a hypothesized internal branch without computing an overall tree and to visualize the phylogenetic content of a sequence alignment.
The main purpose of the TREE-PUZZLE package is to reconstruct trees. It uses the quartet puzzling algorithm as described by Strimmer and von Haeseler.
Key Features
- Fast tree search algorithm.
- Quartet puzzling.
- Automatically assigns estimations of support to each internal branch.
- Incorporates rate heterogeneity in all models of substitution (nucleotides: SH, GTR, TN, HKY, F84, and submodels; amino acids: Dayhoff, JTT, mtREV24, BLOSUM 62, VT, and WAG; two-state data: F81).
- GTR model.
- Analysis:
- Tree Reconstruction using quartet puzzling.
- Likelihood mapping.
- Usertree Evaluation and testing.
- Consensus tree construction.
- Parameter estimation and pairwise distances.
- Consensus tree construction for user given sets of trees.
- Parallel parameter estimation.
- Conducts a number of statistical tests on the data set:
- Chi-square test for homogeneity of base composition.
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- Likelihood ratio to test the clock hypothesis.
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- Kishino-Hasegawa test.
- Weighting scheme of quartets.
- Detects sequences that occur more than once in the data and that therefore can be removed from the data set to speed up analysis.
Website: www.tree-puzzle.de
Support: Manual
Developer: Heiko A. Schmidt, Korbinian Strimmer, Martin Vingron, Arndt von Haeseler, John-von-Neumann
License: GNU General Public License v2.0
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