1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
|
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer>
<email>ribosome@gentoo.org</email>
<name>Olivier Fisette</name>
</maintainer>
<herd>sci</herd>
<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>
|
GitWeb
