Full description
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.
Packages