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