<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<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>