28 lines
1.5 KiB
XML
28 lines
1.5 KiB
XML
<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
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<pkgmetadata>
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<maintainer type="project">
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<email>sci-biology@gentoo.org</email>
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<name>Gentoo Biology Project</name>
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</maintainer>
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<longdescription>
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TREE-PUZZLE is a computer program to reconstruct phylogenetic trees
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from molecular sequence data by maximum likelihood. It implements a
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fast tree search algorithm, quartet puzzling, that allows analysis of
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large data sets and automatically assigns estimations of support to
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each internal branch. TREE-PUZZLE also computes pairwise maximum
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likelihood distances as well as branch lengths for user specified
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trees. Branch lengths can be calculated under the clock-assumption. In
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addition, TREE-PUZZLE offers a novel method, likelihood mapping, to
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investigate the support of a hypothesized internal branch without
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computing an overall tree and to visualize the phylogenetic content of
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a sequence alignment. TREE-PUZZLE also conducts a number of statistical
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tests on the data set (chi-square test for homogeneity of base
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composition, likelihood ratio clock test, Kishino-Hasegawa test). The
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models of substitution provided by TREE-PUZZLE are TN, HKY, F84, SH for
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nucleotides, Dayhoff, JTT, mtREV24, VT, WAG, BLOSUM 62 for amino acids,
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and F81 for two-state data. Rate heterogeneity is modeled by a discrete
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Gamma distribution and by allowing invariable sites. The corresponding
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parameters can be inferred from the data set.
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</longdescription>
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</pkgmetadata>
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