17 lines
1.2 KiB
Plaintext
17 lines
1.2 KiB
Plaintext
TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from
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molecular sequence data by maximum likelihood. It implements a fast tree search
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algorithm, quartet puzzling, that allows analysis of large data sets and
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automatically assigns estimations of support to each internal branch.
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TREE-PUZZLE also computes pairwise maximum likelihood distances as well as
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branch lengths for user specified trees. Branch lengths can be calculated under
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the clock-assumption. In addition, TREE-PUZZLE offers a novel method, likelihood
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mapping, to investigate the support of a hypothesized internal branch without
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computing an overall tree and to visualize the phylogenetic content of a
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sequence alignment. TREE-PUZZLE also conducts a number of statistical tests on
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the data set (chi-square test for homogeneity of base composition, likelihood
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ratio clock test, Kishino-Hasegawa test). The models of substitution provided by
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TREE-PUZZLE are TN, HKY, F84, SH for nucleotides, Dayhoff, JTT, mtREV24, VT,
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WAG, BLOSUM 62 for amino acids, and F81 for two-state data. Rate heterogeneity
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is modeled by a discrete Gamma distribution and by allowing invariable sites.
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The corresponding parameters can be inferred from the data set.
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