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PUZZLE is an application to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. It 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. Rate heterogeneity (invariable sites plus Gamma distributed rates) is incorporated in all models of substitution available (nucleotides: TN, HKY, F84, and submodels; amino acids: Dayhoff, JTT, mtREV24). All model parameters including rate heterogeneity can be estimated from the data by maximum likelihood. PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. In addition, PUZZLE offers a novel method, likelihood mapping, to investigate the support of internal branches without computing an overall tree.

Current Version:   3.1

License Type:   Free

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