TREE-PUZZLE

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.

Features include:

• 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
• Likelihood ratio to test the clock hypothesis
• 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

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Last Updated Saturday, April 13 2013 @ 04:13 PM EDT