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TREEPUZZLE 5.0
TREEPUZZLE 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. TREEPUZZLE also computes pairwise maximum likelihood
distances as well as branch lengths for user specified trees. Branch
lengths can also be calculated under the clockassumption. In addition,
TREEPUZZLE 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.
TREEPUZZLE also conducts a number of statistical tests on the data set
(chisquare test for homogeneity of base composition, likelihood ratio
to test the clock hypothesis, KishinoHasegawa test). The models of
substitution provided by TREEPUZZLE are TN, HKY, F84, SH for
nucleotides, Dayhoff, JTT, mtREV24, BLOSUM 62, VT, WAG for amino acids,
and F81 for twostate data. Rate heterogeneity is modelled by a
discrete Gamma distribution and by allowing invariable sites.
The corresponding parameters can be inferred from the data set.
INSTALLATION
For compile an intall instructions see INSTALL and doc/manual.html
In most cases on UNIX machines the following should work:
sh ./configure
make
make intall
