treepuzzle - Maximum likelihood phylogeny reconstruction using quartets

Property Value
Distribution FreeBSD 12
Repository FreeBSD Ports Latest amd64
Package filename treepuzzle-5.2.txz
Package name treepuzzle
Package version 5.2
Package release -
Package architecture amd64
Package type txz
Category biology
License -
Download size 170.98 KB
Installed size 354.95 KB
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.


Package Version Architecture Repository
treepuzzle-5.2.txz 5.2 i386 FreeBSD Ports Quarterly
treepuzzle-5.2.txz 5.2 amd64 FreeBSD Ports Quarterly
treepuzzle-5.2.txz 5.2 i386 FreeBSD Ports Latest
treepuzzle - - -


Type URL
Binary Package treepuzzle-5.2.txz
Source Package biology/treepuzzle

Install Howto

Install treepuzzle txz package:

# pkg install treepuzzle

See Also

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