From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-biology/tree-puzzle/metadata.xml | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 sci-biology/tree-puzzle/metadata.xml (limited to 'sci-biology/tree-puzzle/metadata.xml') diff --git a/sci-biology/tree-puzzle/metadata.xml b/sci-biology/tree-puzzle/metadata.xml new file mode 100644 index 000000000000..4a34df848e3a --- /dev/null +++ b/sci-biology/tree-puzzle/metadata.xml @@ -0,0 +1,28 @@ + + + + + sci-biology@gentoo.org + Gentoo Biology Project + + + 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. + + -- cgit v1.2.3