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Install

Install this package:

emerge -a sci-biology/tree-puzzle

If the package is masked, you can unmask it using the autounmask tool or standard emerge options:

autounmask sci-biology/tree-puzzle

Or alternatively:

emerge --autounmask-write -a sci-biology/tree-puzzle

Package Information

Description:

TREE-PUZZLE is a computer program 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. TREE-PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can 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. TREE-PUZZLE also conducts a number of statistical tests on the data set (chi-square test for homogeneity of base composition, likelihood ratio clock test, Kishino-Hasegawa test). The models of substitution provided by TREE-PUZZLE are TN, HKY, F84, SH for nucleotides, Dayhoff, JTT, mtREV24, VT, WAG, BLOSUM 62 for amino acids, and F81 for two-state data. Rate heterogeneity is modeled by a discrete Gamma distribution and by allowing invariable sites. The corresponding parameters can be inferred from the data set.

Homepage:

http://www.tree-puzzle.de

License:

GPL-2

Versions

Metadata

Description

• TREE-PUZZLE is a computer program 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. TREE-PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can 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. TREE-PUZZLE also conducts a number of statistical tests on the data set (chi-square test for homogeneity of base composition, likelihood ratio clock test, Kishino-Hasegawa test). The models of substitution provided by TREE-PUZZLE are TN, HKY, F84, SH for nucleotides, Dayhoff, JTT, mtREV24, VT, WAG, BLOSUM 62 for amino acids, and F81 for two-state data. Rate heterogeneity is modeled by a discrete Gamma distribution and by allowing invariable sites. The corresponding parameters can be inferred from the data set.

Maintainers

• Gentoo Biology Project (sci-biology@gentoo.org) - Type: project

<pkgmetadata>
	<maintainer type="project">
		<email>sci-biology@gentoo.org</email>
		<name>Gentoo Biology Project</name>
	</maintainer>
	<longdescription>
		TREE-PUZZLE is a computer program 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. TREE-PUZZLE also computes pairwise maximum
		likelihood distances as well as branch lengths for user specified
		trees. Branch lengths can 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. TREE-PUZZLE also conducts a number of statistical
		tests on the data set (chi-square test for homogeneity of base
		composition, likelihood ratio clock test, Kishino-Hasegawa test). The
		models of substitution provided by TREE-PUZZLE are TN, HKY, F84, SH for
		nucleotides, Dayhoff, JTT, mtREV24, VT, WAG, BLOSUM 62 for amino acids,
		and F81 for two-state data. Rate heterogeneity is modeled by a discrete
		Gamma distribution and by allowing invariable sites. The corresponding
		parameters can be inferred from the data set.
	</longdescription>
</pkgmetadata>

Lint Warnings

• [Warning] USE flag 'mpi' in ebuild 5.2-r1 is not documented in metadata.xml
• [Error] Missing md5-cache for ebuild tree-puzzle-5.2-r1

USE Flags

Manage flags for this package: euse -i <flag> -p sci-biology/tree-puzzle | euse -E <flag> -p sci-biology/tree-puzzle | euse -D <flag> -p sci-biology/tree-puzzle

Files

• tree-puzzle-5.2-C99-decls.patch
• tree-puzzle-5.2-MPI-3.0.patch
• tree-puzzle-5.2-configure-c99.patch

Manifest